title: WT5_xl_5_CpG_2U_180min_refill_at_90min_NP-seq

data_processing:
basecalling with Guppy v3.2.2
Library strategy: ODM-seq
ODM-seq analysis for Nanopore-seq data  We called the bases with Albacore (Oxford Nanopore Technologies, version 2.3.3) or Guppy (Oxford Nanopore Technologies, version 3.2.2), for WT4 and WT5, respectively, and mapped the reads with minimap2 (version 2.14-r892-dirty, (Li 2018)). For methylation calling we used Nanopolish (version 0.11.0, (Simpson et al. 2017)). At each CpG methylation site, the occupancy is calculated as ratio of unmethylated reads over the sum of methylated and unmethylated reads, ignoring reads where the site has been called "ambiguous" by Nanopolish. We ignored methylation sites with a coverage less than 20. Note that, currently, Nanopolish groups CpG sites within 10 bp into one site, thus having a lower resolution than BS-seq.
tsv files contain columns with the absolute occupancy value, the strand, the motif and the number of converted as well as the total number of reads for each methyation site.
Genome_build: SacCer3
Supplementary_files_format_and_content: bedGraph. Tsv

value: 5 min


title: rad16_UV2hr_rep2_A5

status: Public on Nov 27 2019

type: SRA

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

country: USA

institute: Washington State University

description: Replicate 2

library_source: genomic

data_processing:
Library strategy: CPD-seq
Base calling by Torrent_Suite 5.0.4
Fastq files were separated into individual libraries using A1-A6 barcodes, and the barcode sequences were trimmed, as well as the 3' nucleotide of the sequencing read, using a custom perl script
Fastq files were aligned to the yeast genome (SacCer3 or SacCer3+pUC19) using bowtie2-2.2.6 software to generate SAM files
SAM files were converted to BAM files using samtools
BAM files were converted to BED files using BEDTOOLS2 bamtoBed
Damage coordinates were mapped using custom perl script
Only reads mapping to dipyrimidine sequences (i.e., TT, TC, CT, CC), corresponding to CPD lesions were retained in BED file using custom perl script.
BED files were converted to WIG file using COUNT function of IGVTools
Background values dipyrimidine sequences were generated in WIG file using custom perl script
Genome_build: SacCer3
Supplementary_files_format_and_content: WIG files containing counts of DNA CPD lesion reads filtered for only dipyrimidine mapping sequences and including background value of 0.0 at nucleotides associated with dipyrimidines with no mapped sequencing reads. A sequencing read count was  assigned to each nucleotide in the lesion-containing dipyrimidine sequence.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: Yeast cultures (BY4741) were grown in YPD (yeast extract, peptone, dextrose) to OD600=~0.8 in a yeast shaker.

extract_protocol:
Yeast genomic DNA was extracted by mixing cell pellets with 250 μl of DNA lysis buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 10 mM Tris-HCl pH 8.0, 1 mM EDTA), 250 μl of PCI (Phenol:Chloroform:Isoamyl Alcohol=25:24:1), and 150 μl of acid-washed glass beads, and vortexed vigorously twice, 2 min each time. After adding 200 μl of TE (10mM Tris-HCl, pH 7.5, 1 mM EDTA) buffer, cell lysates were centrifuged and the supernatant was mixed with 1 ml of ethanol to precipitate DNA at room temperature for 5 min. DNA pellet was dissolved in 200 μl of TE and incubated with 2 μl of RNase A/T1 (ThermoFisher Scientific) at 37˚C for 1 hr to remove RNA. DNA was subsequently purified with PCI extraction, ethanol precipitated, and disolved in sterile deionized H2O. The purified genomic DNA was quantified and 12 μg of DNA was used for each sequencing library preparation.
CPD-seq procedure is adopted from the recently published emRiboSeq method (Nature Protocols 2015 10, 1433–1444). Briefly, DNA fragments were first ligated to a double-stranded adaptor DNA trP1, and free 3'-OHs were blocked by  terminal transferase and dideoxy-ATP.  CPD lesions were  cleaved with T4 endonuclease V and apurinic/apyrimidinic (AP) endonuclease, APE 1, to generage new 3'-OHs. DNA was then ligated to adaptor  A. Up to 6 different barcoded A adaptors (A1: AAGAGGAT; A2: TTCGTGAT; A3: CCTGAGAT; A4: ATCGCGAT; A5: TACTGGAT; and A6: GAACTGAT) were used to generate libraries for different experiments. DNA was purified with Streptavidin beads and amplified for up to 6 cycles in a PCR reaction with primers complimentary to A and trP1, and the resulting DNA libraries were used for DNA sequencing.

treatment_protocol: Cells were collected and resuspended in sterile deionized H2O and irradiated with 125 J/m2 UVC. After UV irradiation, cells were spun down and resuspended in pre-warm YPD medium (yeast extract, peptone, dextrose) for repair. Aliquots (10 ml of yeast culture) were taken before UV irradiation (No UV), immediately after UV irradiation (0hr), and at different repair time points as indicated. Cells were spun down and kept at -80˚C until genomic DNA isolation.

tag: strain

tag: genotype

tag: treatment

value: UV irradiated 125 J/m2

tag: repair time

value: 2 hr


title: veh1

city: Rochester

first: Suowen

last: Xu

state: NY

address: 603 Elmwood Avenue

department: Medicine

institute: University of Rochester

library_source: transcriptomic

data_processing:
DATA FORMATTING (Illumina -> FastQ) & DEMULTIPLEXING - bcltofastq-2.19.0
CLEANING - Trimmomatic-0.36 “TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:35”
MAPPING - STAR_2.6.0c “--twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical”
READ COUNTING - subread-1.6.1 “featurecounts, -s 2 -t exon -g gene_name”
Genome_build: GRCh38.p12 (hg38) + Gencode-28 Annotation
Supplementary_files_format_and_content: normalized abundance

molecule: total RNA

organism: Homo sapiens

growth_protocol: Human umbilical vein endothelial cells (HUVECs, Cell Application Inc.) were cultured in M200 media supplemented with 5% FBS, 1X ECGS ( Cell Application Inc.) and 1X antibiotics.

extract_protocol:
Total RNA was harvested using RNAeasy Mini Kit from Qiagen. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Confluent HUVECs were treated with BRD4 inhibitor (+)-JQ1 (10 uM, in 0.1% DMSO) for 48 h before RNA was collected for genome-wide RNA-sequencing, n=2 different donors.

tag: cell type

value: Human umbilical vein endothelial cells (HUVECs)

value: vehicle control


title: Neutrophils, CT8 (J)

city: Baltimore

first: Jose

middle: M

last: Adrover

state: Maryland

address: 855 N Wolfe St

department: Cell Biology

institute: Johns Hopkins University

description:
Neutrophils extracted at 8am
J_CT14

data_processing:
Illumina bcl2fastq 2.20 software used for basecalling
Genome_build: Ensembl genebuild 76 (mouse assembly GRCm38).
Supplementary_files_format_and_content: normalized_cpm_humanRNAseq.csv (normalized counts per million )

molecule: polyA RNA

source_name: Neutrophils from blood

growth_protocol: Human volunteers

extract_protocol: RNA libraries were prepared for sequencing using NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina

treatment_protocol: Healthy volunteers

tag: disease state

value: Healthy

tag: tissue

value: Blood

value: neutrophil

tag: time of extraction


title: CREB1

city: Huntsville

first: Eric

last: Mendenhall

state: AL

address: 601 Genome Way Northwest

institute: HudsonAlpha Institute

description:
Re-analysis of:
GSM2533926 GSM2533925
Raw file(s):
ENCFF517FOY ENCFF951QJT
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR331ORD

data_processing:
Fastq files were downloaded from ENCODE portal (https://www.encodeproject.org/) for 2 replicates and 2 controls
ChIP-seq fastqs and ChIP-seq controls were aligned to hg19 genome assembly using BWA-0.7.12(Burrows Wheeler Aligner)
Post-alignment filtering was performed using samtools with MAPQ_THRESH=30 & picard-tools-1.88 to remove the duplicates
Peak enrichment was computed using phantompeakqualtools, implementing SPP peak calling algorithm, to generate narrowpeaks
IDR was run on replicates peak file and pooled peaks, using idr-2.0.2 tool, to generate peaks passing IDR cutoff 0.02 (soft-idr-threshold) followed by filtering of ENCODE blacklisted regions
Genome_build: hg19 male
Supplementary_files_format_and_content: NarrowPeak files are in BED6+4 format with 10 tab-delimited columns [chrom ,chromStart ,chromEnd ,name ,score ,strand ,signalValue ,pValue(-log10) ,qValue(-log10) , peak]; -1 used if no pValue, qValue assigned.

source_name: HepG2 cells

growth_protocol: HepG2 were grown according to the approved ENCODE cell culture protocols (http://hgwdev.cse.ucsc.edu/ENCODE/protocols/cell)

extract_protocol:
Cross-linked chromatin was immunoprecipitated with an antibody. The Protein:DNA crosslinks were then reversed and the DNA fragments were recovered and sequenced. Please see protocol notes below and go to http://hudsonalpha.org/myers-lab/protocols for the most current version of the protocol.
Illumina Single End for ChIP-seq

tag: cell line

tag: chip antibody


title: CREM

description:
Re-analysis of:
GSM2534611 GSM2534612
Raw file(s):
ENCFF070RQL ENCFF779OCL
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR903ELW

value: CREM


title: rad16_2hrUV_A5

description: Replicate 1


title: rad16_UV0hr_rep2_A4

description: Replicate 2

value: 0 hr


title: CIZ1

description:
Raw file(s):
ENCFF527ZJY_in_progress ENCFF431TWM_in_progress
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR586QSA https://www.encodeproject.org/experiments/ENCSR586QSA


title: HHEX

description:
Re-analysis of:
GSM2534267 GSM2534266
Raw file(s):
ENCFF134IZQ ENCFF096HOR
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR656JZL

value: FLAG-HHEX


title: Neutrophils, CT14 (J)

description:
Neutrophils extracted at 14pm
J_CT8


title: CEBPG

description:
Re-analysis of:
GSM2534242 GSM2534241
Raw file(s):
ENCFF430LJV ENCFF608JCC
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR639IIZ

value: FLAG-CEBPG


title: rad16_0hrUV_A4

description: Replicate 1


title: Control [RNA-seq]

city: Suwon

first: Dongho

last: Kim

address: #300 Chunchun-dong, Jangan-Ku, Suwon, Kyungggi-do

department: Samsung Biomedical Research Institute

country: South Korea

institute: Sungkyunkwan University School of Medicine

data_processing:
After sequencing, the low-quality reads and PCR duplicates were removed by Trimmomatic 0.38.
The trimmed sequences were then assembled into reference transcripts using the HISAT2 program.
The read count was normalized into a value of FPKM (Fragments Per Kilobase of transcript per Million mapped reads), and the reads with a value of zero were excluded.
Significantly up- or down-regulated genes were identified by cutoff value of |FC| >= 1.5.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.gene_abund.anno.tab: Tab-delimited text files include FPKM and TPM values.

source_name: H1299 cells

growth_protocol: The lung cancer cell line H1299 (ATCC, CRL-5803) was obtained from the American Type Culture Collection (ATCC). The cells were cultured in RPMI 1640 medium (Lonza, Allendale, NJ) supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin, and 100 μg/mL streptomycin, at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA was isolated from cultured H1299 cells using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA). DNA contamination was removed using DNase, and the remaining RNA was broken into short fragments. The RNA fragments were reverse transcribed into cDNA, ligated with adaptors, and PCR amplified. The amplified cDNAs were then selected by a range of sizes and sequenced using a next-generation sequencing device (NovaSeq 6000 System).
The sequence library was mapped to the reference genome UCSC hg19 using the Bowtie2 program.

treatment_protocol: The cells were treated with or without 5mM metformin (D150959, Sigma-Aldrich, St. Louis, MO).

value: Non-small cell lung cancer cell line

tag: passages


title: Neutrophils, CT14 (E)

description:
Neutrophils extracted at 14pm
E_CT8


title: Neutrophils, CT8 (E)

description:
Neutrophils extracted at 8am
E_CT14


title: CEBPA

description:
Re-analysis of:
GSM2527515 GSM2527514
Raw file(s):
ENCFF782RSZ ENCFF460NRJ
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR142IGM

value: FLAG-CEBPA


title: CBX1


title: Neutrophils, CT8 (C)

description:
Neutrophils extracted at 8am
C_CT14


title: BCL6_iso1

description:
Re-analysis of:
GSM2534405 GSM2534404
Raw file(s):
ENCFF914FOC ENCFF948EZE
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR759BDG


title: 468.DMSO-R

type: protein

city: New York

first: Ramon

last: Parsons

state: New York

address: 1425 Madison Ave, L1-15C

department: Oncological Sciences

institute: Icahn school of medicine at Mount Sinai

hyb_protocol: Samples were probed with antibodies by tyramide-based signal amplification approach and visualized by DAB colorimetric reaction

scan_protocol: Slides were scanned on a flatbed scanner to produce 16-bit tiff image. Spots from tiff images were identified and the density was quantified by Array-Pro Analyzer.

data_processing:
Each dilution curve was fitted with a logistic model (“SuperCurve Fitting” developed at MDACC) and normalized by median polish. The data clustering was performed using Cluster 3.0 (centered by gene; followed by hierarchically clustering by gene and array using complete linkage) and TreeView.
Relative protein levels for each sample were determined by interpolation of each dilution curves from the standard curve (supercurve) of the slide (antibody).  Supercurve is constructed by a script in R, written by Bioinformatics.  These values (given as Log2 values) are defined as Supercurve Log2 (Raw) values and shown in the  file named RawLog2.

label: tyramide-based signal amplification

molecule: protein

source_name: MDA-MB-468 cells treated with DMSO

label_protocol: Using a 2470 Arrayer (Aushon BioSystems, tumor or normal tissue lysates were serially diluted 2-fold for 5 dilutions (From undiluted to 1:16 dilutio) and arrayed on nitrocellulose-coated FAST slides in an 11X11 format. Samples were probed with antibodies using the Dako CSA tyramide-amplification approach and visualized by DAB colorimetric reaction.

growth_protocol: 2E6 MDA-MB-468 and PC-3 cell lines were seeded in 10 cm dishes.

extract_protocol: Cell lysates were collected using IP lysis buffer, and adjust protein concentration to 1.5 ug/ul. Mix the cell lysate with (4XSDS + B‐Me) sample buffer without bromophenol blue (3 parts of cell lysate plus one part of 4XSDS sample buffer). Boil the samples for 5 minutes, and store in –80 C until sample submission.

treatment_protocol: Cells were treated with DMSO, AZD5363 (AZD), MS21 (021) at 1µM for 24hr respectively.

value: Triple negative breast cancer cell line


title: 468.AZD-R

source_name: MDA-MB-468 cells treated with AZD 5363


title: PC-3.021-R

source_name: PC-3 cells treated with MS21

value: Prostate cancer cell line


title: 468.021-R

source_name: MDA-MB-468 cells treated with MS21


title: ZNF219


title: PC-3.DMSO-R

source_name: PC-3 cells treated with DMSO


title: ATF4

description:
Re-analysis of:
GSM2534290 GSM2534291
Raw file(s):
ENCFF444RSD ENCFF240REY
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR669LCD


title: TCF25


title: ASH2L

description:
Raw file(s):
ENCFF210PXS_in_progress ENCFF525AYL_in_progress
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR508LMH https://www.encodeproject.org/experiments/ENCSR508LMH


title: ARID4B

description:
Re-analysis of:
GSM2534717 GSM2534716
Raw file(s):
ENCFF362DJJ ENCFF550QWK
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR988LZG


title: KDM1A

description:
Raw file(s):
ENCFF750VZA ENCFF215QNG
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR115BLD


title: wt_NoUV_A1

value: Wild-type


title: Neutrophils, CT14 (C)

description:
Neutrophils extracted at 14pm
C_CT8


title: 468.021


title: ATF1

description:
Re-analysis of:
GSM2527636 GSM2527635
Raw file(s):
ENCFF038RNL ENCFF853ECX
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR253OON


title: FOXO1


title: BRD4

description:
Raw file(s):
ENCFF953UBF ENCFF946FEX
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR514EOE


title: 468.AZD


title: 468.DMSO


title: Mix4

city: Nanjing

first: Xinlei

last: Zhao

address: Sipailou 2

country: China

institute: Southeast University

data_processing:
Illumina Casava1.7 software used for basecalling.
Filter raw reads  using software fastp with default parameters. Adapters and polyA tails were trimmed , followed by that read two was mapped to GRCh38 and mm10 reference genome with ensemble version 92 gene annotation using STAR with default parameters.
Reads with the same cell barcode, UMI and gene were grouped together to calculate the number of UMIs per gene per cell. Cell number was then determined based on the ‘knee’ method.
The dropseq beads were used in the experiments with 12bp random cell barcode (basepairs 1-12) and 8 bp random UMI sequences (basepairs 13-20). Barcode and UMI are included only in R1.
Genome_build: GRCh38, mm10
Supplementary_files_format_and_content: tab-delimited text files include reads counts of each gene for each cell in each sample. Gene IDs include both human and mouse genes.  The human genes identified by the gene names in all capital letters, i.e. MID1, and mouse genes identified by a capital letter followed by lower case letters, i.e. Mid1.

organism:
Homo sapiens
Mus musculus

extract_protocol:
Four cell lines were cultured separately in DMEM (Thermo Fisher Gibco) with 10% fetal bovine serum (FBS) (Thermo Fisher Gibco), and 1% penicillin-streptomycin (Beyotime Biotechnology) in an incubator with 5% carbon dioxide at 37°C. Single cell suspension with 1×105 cells/mL in concentration in PBS (HyClone) were prepared.
scRNA-seq libraries were constructed following Singleron GEXSCOPETM protocol using GEXSCOPETM Single Cell RNA Library Kit (Singleron).  Cells from independent cell lines were not associated with barcodes prior to library construction so there is no key available to link cell line ID to cell barcode.


title: Mix3


title: PC-3.AZD-R

source_name: PC-3 cells treated with AZD 5363


title: U343_Riboseq_T1_replicate_3 [U343_L3_5GY_T1_S17_L002]

status: Public on Nov 26 2019

city: San Antonio

first: David

last: Kadosh

state: Texas

address: 7703 Floyd Curl Dr., MC: 7758

department: Department of Microbiology, Immunology & Molecular Genetics

institute: University of Texas Health Science Center at San Antonio

data_processing:
Adaptor sequences and low-quality score (phred quality score < 5) bases were trimmed from RNA-Seq and Ribo-Seq datasets with TrimGalore (v0.4.3)
The trimmed Ribo-seq reads were aligned to the human reference genome sequence (Ensembl GRCh38.p7) using STAR aligner (v.2.5.2b) with  GENCODE v25 as a guided reference annotation, allowing a mismatch of at most two positions  --outFilterMismatchNmax 2. For RNA-seq STARlong was used allowing a total of 100 mismatches (--outFilterMismatchNmax 100) and aminimum match of 66% (--outFilterMatchNminOverLread 0.66)
Read abundance files were generated using htseq-count. For Ribo-seq samples only CDS was used for counting, while Ribo-seq samples were counted using both CDS and 'exon' as targets.
Genome_build: hg38
Supplementary_files_format_and_content: raw counts table

growth_protocol: U251 and U343 cells were obtained from the University of Uppsala (Sweden) and maintained in Dulbecco’s Modified Eagle Medium (DMEM, Hyclone) supplemented with 10% fetal bovine serum, 1% Penicillin/Streptomycin  at 37C in  5% CO2-humidified incubators and were sub-cultured twice a week.

extract_protocol:
RNA was purified using a GeneJet RNA kit from Thermo Scientific. The TruSeq Ribo Profile (Mammalian) kit from Illumina was used to prepare material for ribosome profiling (Ribo-seq). RNA-seq and Ribo-seq samples were prepared according to Illumina protocols and sequenced at UTHSCSA Genome Sequencing Facility.
RNA-seq and Ribo-seq samples were prepared according to Illumina protocols and sequenced at UTHSCSA Genome Sequencing Facility.

treatment_protocol: Cells were plated after appropriate dilution, and ionizing radiation treatment was performed on the next day at a dose of 5 Gray (Gy). A cabinet X-ray system (CP-160 Cabinet X-Radiator; Faxitron X-Ray Corp., Tucson, AZ) was used. After exposure to ionizing radiation, cells were cultured for 1 and 24 hours (hrs).

value: glioblastoma cell line

tag: tissue source

value: brain/CNS

tag: disease

value: Glioblastoma,ud

value: Grade IV

tag: ethinicity

value: caucasian


title: U343_Riboseq_T24_replicate_3 [U343_L3_5GY_T24_S18_L002]


title: PC-3.AZD


title: PC-3.DMSO


title: U343_Riboseq_T1_replicate_2 [U343_L2_5GY_T1_S14_L002]


title: U343_Riboseq_T0_replicate_2 [U343_L2_0GY_T0_S13_L002]


title: U343_Riboseq_T0_replicate_3 [U343_L3_0GY_T0_S16_L002]


title: U343_Riboseq_T24_replicate_2 [U343_L2_5GY_T24_S15_L002]


title: U343_Riboseq_T24_replicate_1 [U343_L1_5GY_T24_S12_L002]


title: RING1

description:
Re-analysis of:
Raw file(s):
ENCFF119HIP_in_progress ENCFF828ZEQ_in_progress
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR399EFZ https://www.encodeproject.org/experiments/ENCSR399EFZ_in_progress
Note, two different instrument models: ENCFF119HIP_in_progress (Illumina HiSeq 2000) ENCFF828ZEQ_in_progress (Illumina HiSeq 2500).


title: U343_Riboseq_T0_replicate_1 [U343_L1_0GY_T0_S10_L002]


title: U251_Riboseq_T24_replicate_3 [U251_L3_5GY_T24_S9_L001]


title: PC-3.021


title: U251_Riboseq_T24_replicate_2 [U251_L2_5GY_T24_S6_L001]


title: BMI1

description:
Raw file(s):
ENCFF278LUX_in_progress ENCFF927XKT_in_progress
can be retrieved from ENCODE:
https://www.encodeproject.org/experiments/ENCSR135ZVC https://www.encodeproject.org/experiments/ENCSR135ZVC


title: U251_Riboseq_T1_replicate_3 [U251_L3_5GY_T1_S8_L001]


title: U251_Riboseq_T0_replicate_2 [U251_L2_0GY_T0_S4_L001]


title: U251_Riboseq_T1_replicate_2 [U251_L2_5GY_T1_S5_L001]


title: U343_RNAseq_T0_replicate_3 [U343_L3_T0_S28]


title: U251_Riboseq_T0_replicate_1 [U251_TC1_0GY_T0_S1_L001]


title: U343_RNAseq_T24_replicate_3 [U343_L3_T24_S30]


title: U343_RNAseq_T1_replicate_3 [U343_L3_T1_S29]


title: U251_Riboseq_T1_replicate_1 [U251_TC1_5GY_T1_S2_L001]


title: U251_Riboseq_T24_replicate_1 [U251_TC1_5GY_T24_S3_L001]


title: U343_RNAseq_T1_replicate_2 [U343_L2_T1_S26]


title: U251_RNAseq_T24_replicate_3 [U251_L3_T24_S21]


title: U343_RNAseq_T0_replicate_2 [U343_L2_T0_S25]


title: U343_RNAseq_T24_replicate_1 [U343_L1_T24_S24]


title: U343_RNAseq_T1_replicate_1 [U343_L1_T1_S23]


title: U251_RNAseq_T1_replicate_1 [U251_L1_T1_S14]


title: U251_RNAseq_T1_replicate_2 [U251_L2_T1_S17]


title: U251_RNAseq_T24_replicate_2 [U251_L2_T24_S18]


title: U251_RNAseq_T0_replicate_2 [U251_L2_T0_b_S16]


title: U251_RNAseq_T0_replicate_1 [U251_L1_T0_S13]


title: U251_RNAseq_T24_replicate_1 [U251_L1_T24_S15]


title: U343_Riboseq_T1_replicate_1 [U343_L1_5GY_T1_S11_L002]


title: TRA2B-OE_replicate_3

city: Farmington

first: Marina

last: Yurieva

state: Connecticut

address: 10 Discovery dr

department: Computational Sciences

institute: Jackson Laboratory

data_processing:
Paired-end reads were preprocessed for trimming of low-quality regions by Trimmomatic (v. 0.36) (Bolger et al., 2014)
Trimmed reads mapped to the human reference genome using STAR (v.2.5.1b) (Dobin et al., 2013), in 2-pass mode with the Gencode GRCh37 v.25 reference transcript annotation
Raw counts were calculated using featureCounts (http://subread.sourceforge.net/)
Genome_build: GRCh37 v.25
Supplementary_files_format_and_content: raw counts for each sample in a table

growth_protocol: MCF-10A cells stably expressing a retroviral construct containing the coding sequence of SRSF2, SRSF4, SRSF6, SRSF9, TRA2B, or a control empty vector plasmid (PWZL), were grown for 8 days in matrigel.

extract_protocol:
3D structures were removed from the matrigel and RNA was extracted using an RNAeasy extraction kit (Qiagen) which includes DNAseI treatment.
Libraries were prepared using the RNA-seq stranded mRNA kit from Illumina and sequenced as 101 PE reads on a HiSeq 2000

tag: construct

tag: condition

value: 3D culture day 8

tag: barcode

value: ATGTCA


title: TRA2B-OE_replicate_1


title: SRSF9-OE_replicate_1

value: CCGTCC


title: SRSF9-OE_replicate_2


title: TRA2B-OE_replicate_2


title: U343_RNAseq_T24_replicate_2 [U343_L2_T24_S27]


title: SRSF6-OE_replicate_2

value: ACAGTG


title: SRSF6-OE_replicate_3


title: SRSF6-OE_replicate_1


title: SRSF4-OE_replicate_2

value: GTGAAA


title: SRSF4-OE_replicate_3


title: SRSF2-OE_replicate_3

value: TGACCA


title: SRSF2-OE_replicate_2


title: SRSF4-OE_replicate_1


title: SRSF2-OE_replicate_1


title: U343_RNAseq_T0_replicate_1 [U343_L1_T0_S22]


title: SRSF9-OE_replicate_3


title: U251_RNAseq_T1_replicate_3 [U251_L3_T1_a_S20]


title: Control_shRNA_+DOX_replicate_3

growth_protocol: MDA-MB231 cells stably expressing a retroviral construct containing a control or TRA2B-targeting DOX inducible shRNAs were grown for 8 days in matrigel.

extract_protocol:
3D structures were removed from the matrigel and RNA was extracted using an RNAeasy extraction kit (Qiagen) which includes DNAseI treatment.
Libraries were prepared using the RNA-seq stranded mRNA kit from Illumina and sequenced as 125 bp PE reads on a HiSeq2500

treatment_protocol: Cells were treated with DOX (2ug/ml) or DMSO. Media was replaced every 3 days.

value: control shRNA

tag: culture

value: with DOX (2ug/ml)


title: Control_replicate_1

value: control vector

value: CGATGT


title: Control_shRNA_+DOX_replicate_1

value: CGATGT(A)


title: Control_replicate_2


title: Control_shRNA_+DOX_replicate_2

value: CCGTCC(C)


title: TRA2B_shRNA1_+DOX_replicate_2

value: TRA2B shRNA 1

value: ACAGTG(A)


title: Control_shRNA_-DOX_replicate_2

value: without DOX

value: GCCAAT(A)


title: TRA2B_shRNA1_-DOX_replicate_3

value: GTGAAA(C)


title: Control_shRNA_-DOX_replicate_1

value: 3D culture day 8


title: TRA2B_shRNA1_+DOX_replicate_1


title: TRA2B_shRNA1_-DOX_replicate_1


title: TRA2B_shRNA2_+DOX_replicate_2

value: TRA2B shRNA 2

value: CAGATC(A)


title: TRA2B_shRNA2_+DOX_replicate_1


title: TRA2B_shRNA1_+DOX_replicate_3


title: Control_replicate_3


title: TRA2B_shRNA2_-DOX_replicate_2


title: TRA2B_shRNA2_-DOX_replicate_3


title: TRA2B_shRNA2_-DOX_replicate_1


title: CXKO-2F-hiSCs (dH1)-1

city: Beijing

first: Jianlin

last: Liang

address: Tsinghua park

department: Medical School

institute: Tsinghua University

data_processing:
Raw data were mapped to human genome build by TopHat (version 2.1.1), reads from PCR duplicates were dropped
The gene expression level was calculated by Cufflinks (version 2.2.1) using the protein coding genes GTF file extracted from Ensembl database (Homo_sapiens.GRCh37.75.gtf).
Read counts were obtained using HTSeq (version 0.9.1).
Differentially expressed genes (DEGs) were analyzed using R package DESeq2 and selected using p-value < 0.01 as a threshold.
Heat map was plotted using heatmap.2 function of R, and gene expressions were scaled to FPKM or Z-scores.
We used R function cor to do sample correlation clustering and K-means clustering was performed using Cluster 3.0 package (K = 3, Spearman Correlation, Complete-linkage) and clustered heat maps were produced by TreeView.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Sertoli like cells

growth_protocol: Sertoli-like cell reprogramming was carried out in a T75 flask coated with Matrigel (1%). In brief, 150000 human fibroblast cells carrying AMH:GFP reporter were seeded into T75 flask 1 day prior to overnight transduction with lentivirus NR5A1, GATA4, DMRT1, SOX9 and WT1 (for 5F-hiSCs) or NR5A1 and GATA4 (for 2F-hiSCs), recovered for 24 hours, following by drug selection with geneticin (1 mg/ml) for 5 days in MEF medium. After drug selection, transduced cells were cultured in DF12 medium, maintained for the indicated reprogramming duration, and harvested for FACS by digestion with TrypLE Express (Invitrogen). The single cell suspension for FACS was prepared with MACS medium (10% FBS in PBS with 0.0125 mM EDTA) and filtrated through a BD cell sorter. Cell sorting was proceeded on a high-speed cell sorter (Influx, BD) and was sorted to collecting tube containing DF12 medium.

extract_protocol:
Cells were collected by FACS and total RNA was extracted by TRIZOL (Invitrogen). The quality and integrity of the purified RNAs was checked by Agilent 2100 bioanalyzer.
Sequencing libraries preparation and sequencing operations were carried out by ANNOROAD, a company providing RNA sequencing service, complied with the whole set of processes from Illumina.

value: CX43 deficient derived Sertoli like cells

tag: passage

tag: reporter


title: TRA2B_shRNA2_+DOX_replicate_3

tag: treatment


title: Control_shRNA_-DOX_replicate_3


title: CXKO-2F-hiSCs (dH1)-2

tag: cell type


title: aSCs-1

source_name: Sertoli cells

value: primary adult Sertoli cells


title: 2F-hiSCs (dH1)-2

value: derived Sertoli like cells


title: aSCs-2


title: 5F-hiSCs (dH1)-1


title: CXKO-dH1-2K7-2

source_name: fibroblasts

value: CX43 deficient ES derived fibroblast


title: 2F-hiSCs (dH1)-1


title: 5F-hiSCs (dH1)-2


title: CXKO-dH1-2K7-1


title: dH1-2K7-2

value: ES derived fibroblast


title: 5F-hiSCs (HPF)


title: dH1-2K7-1


title: TRA2B_shRNA1_-DOX_replicate_2


title: Aarssti/sti #2

city: La Jolla

first: Robert

last: Signer

state: California

address: 3855 Health Sciences Drive

department: Division of Regenerative Medicine

institute: UCSD

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were mapped against the mm10 reference using Tophat v1.4.1 (--library-type fr-firststrand)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed
Genome_build: mm10
Supplementary_files_format_and_content: read count matrix with rows as genes and columns as cells

organism: Mus musculus

source_name: Hematopoietic stem cells

growth_protocol: Mice were housed under specific pathogen free conditions

extract_protocol:
Cells were sorted into RLT+ buffer and RNA was extracted with the Rneasy plus micro kit (Qiagen)
SMARTseq2

treatment_protocol: Hematopoietic stem cells were FACS isolated based on their CD150+CD48-Lineage-Sca1+ckit+ cell surface phenotype

tag: strain

tag: developmental stage

value: Adult

value: bone marrow

value: Hematopoietic stem cell

tag: genotype

value: Aarssti/sti


title: Aars+/+ #3

tag: tissue

value: Aars+/+


title: Aars+/+ #1


title: Aars+/+ #2


title: Aarssti/sti #1


title: Aarssti/sti #3


title: Dnmt3a_cKO1_cell

city: brookline

first: Harrison

middle: Wren

last: Gabel

state: Massachusetts

address: 220 longwood avenue

department: Neurbiology

institute: Harvard Medical School

data_processing:
Raw FASTQ files were trimmed with Trim Galore, using a quality filter of 20, then rRNA sequences were filtered out using Bowtie, using rRNA sequences from Mus Musculus obtained from the NCBI sequence database (see Key Resources Table). The unaligned reads from this step were then aligned to mm9 using STAR (Dobin et al., 2013), using the default parameters. Reads mapping to multiple regions in the genome were then filtered out, and uniquely mapping reads were converted to BED files. Intronic and exonic reads were then separated. To do this, splice-site reads were first filtered out of the BED read files, then reads that mapped entirely within exons were added to the splice-site reads to make the exonic read file. All remaining reads that overlapped introns were considered intronic reads. Finally, reads were assigned to genes using bedtools coverage -counts.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-separated table (with header) of genes, identifiers, and various gene-associated RNA coverage, methylation level, and ChIP signal

source_name: Cortex whole cell

growth_protocol: Brain tissue was taken from DNMT3A Baf53b-cKO and wild-type mice maintained under standard housing conditions.

extract_protocol:
Cerebral cortex 7-8 weeks of age was dissected on ice in phosphate buffer saline. The tissue was flash-frozen in liquid nitrogen and stored at -80°C. Total RNA was extracted from 1/16th of a whole cortex using RLT buffer following RNeasy Micro Kit (Qiagen).
RNA libraries were generated from 250ng total and nuclear RNA with NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB) using a modified amplification protocol (37°C, 15 minutes; 98°C, 30 seconds; (98°C, 10 seconds; 65°C, 30 seconds; 72°C, 30 seconds)x13; 72°C, 5 minutes; 4°C hold. RNA libraries were pooled at a final concentration of 8-10nM
RNA was sequenced using Illumina HiSeq 2500 or 3000 with the Genome Technology Access Center (GTAC) at Washington University in St. Louis, typically yielding 20-30 million single-end reads per sample.

value: Dnmt3a conditional knock out

tag: Sex

value: Male

tag: age

value: 7-8 weeks


title: Dnmt3a_cKO2_cell


title: Dnmt3a_WT2_cell

value: wild type


title: Dnmt3a_WT3_cell

value: Female


title: Dnmt3a_WT4_cell


title: Dnmt3a_cKO3_cell


title: Asf1a_KO_New_1-3

city: New York City

first: Alireza

last: Khodadadi-Jamayran

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

data_processing:
Basecalls performed using CASAVA.
RNA-Seq reads were mapped to mm10 using STAR guided by GTF.
Calculating insert size and standard deviation performed using Picard tools.
RNA-Seq read counting performed using HT-seq.
Normalization and differential expression analyses performed using DEseq2.
BAM to bedgraph performed using bedtools.
bedgraph to bigwig performed using bedGraphToBigWig v4.
Statistics and plotting performed in R v3.3.0.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_ct_genes.txt: Count tables

source_name: KP lung tumor cell

growth_protocol: KrasG12D/P53-/-(KP)-Cas9 single clone was transfected with ctrl vector, ctrl sgRNA-1, ctrl-sgRNA-2 or ctrl-sgRNA-3 and then selected by using 5ug/ml Blasticidin, to get the 4 ctrl lines; KP-Cas9 single clone was transfected with Asf1a sgRNA-1, sgRNA-2, sgRNA-3 and new sgRNA-1 and then selected by using 5ug/ml Blasticidin, and then picked up single clones with Asf1a KO. For each Asf1a sgRNA, we selected one clone for RNA seq, so totally we have 4 Asf1a KO clones for RNA seq.

extract_protocol: Extract total RNA by using RNeasy Plus Mini Kit (Qiagen).

treatment_protocol: Control group (Vector, Ctrl-1, Ctrl-2, Ctrl-3) is Asf1a WT; KO group (KO_1-3, KO_2-1, KO_3-4, KO_New_1-3) is Asf1a KO.

value: KP lung tumor cells

tag: sample type

value: In vitro cultured cell line

tag: strain/background

tag: genotype/variation

value: Asf1a KO


title: Control 2

value: Asf1a WT


title: Vector


title: Control 3


title: Asf1a_KO_2-1


title: Control 1


title: Dnmt3a_WT1_cell


title: HPF-2K7

source_name: pulmonary fibroblast

value: primary fibroblast


title: Asf1a_KO_3-4


title: KOWT_KO6_nuclear

source_name: Cortex nucleus

growth_protocol: Brain tissue was taken from MeCP2 knockout, overexpression, and wild-type mice maintained under standard housing conditions.

extract_protocol:
Cerebral cortex 7-10 weeks of age was dissected on ice in phosphate buffer saline. The tissue was flash-frozen in liquid nitrogen and stored at -80°C. Total RNA was extracted from 1/16th of a whole cortex using RLT buffer following RNeasy Micro Kit (Qiagen). Nuclear RNA was isolated following a modified version of the protocol described by Mo et al., 2015. Briefly, half of a cortex was homogenized in 0.25M sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH using a glass dounce homogenizer. Nuclei were isolated via centrifugation at 10,000g for 18 minutes at 4°C (Sorvall HB-4) by pelleting through a 30% iodixanol density gradient (Sigma D1556). RNA was isolated from nuclei by resuspending pellet in RLT buffer following the RNeasy Micro Kit (Qiagen).
RNA libraries were generated from 250ng total and nuclear RNA with NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB) using a modified amplification protocol (37°C, 15 minutes; 98°C, 30 seconds; (98°C, 10 seconds; 65°C, 30 seconds; 72°C, 30 seconds)x13; 72°C, 5 minutes; 4°C hold. RNA libraries were pooled at a final concentration of 8-10nM
RNA was sequenced using Illumina HiSeq 2500 or 3000 with the Genome Technology Access Center (GTAC) at Washington University in St. Louis, typically yielding 20-30 million single-end reads per sample.

value: MeCP2 knock out


title: KOWT_WT2_cell


title: KOWT_KO4_nuclear


title: Asf1a_KO_1-3


title: KOWT_KO2_cell


title: KOWT_KO5_nuclear


title: Dnmt3a_cKO4_cell


title: KOWT_KO2_nuclear


title: KOWT_KO3_nuclear


title: KOWT_WT5_nuclear


title: KOWT_WT4_nuclear


title: KOWT_WT2_nuclear


title: KOWT_WT3_nuclear


title: KOWT_WT1_nuclear


title: KOWT_WT6_nuclear


title: EK02004: HT29GFP + R568

city: vienna

first: luca

last: iamartino

state: Please Select

address: Waehringer Guertel 18-20

country: Austria

institute: Institute of Pathophysiology and Allergy Research

data_processing:
Raw intensities data from NextSeq 500 were basecalled and demultiplexed using Illumina bcl2fastq v2.19.1.403 to output fastq files per sample.
Reads in fastq format were aligned to the human reference genome version GRCh38 which was complemented with additional sequences for the lentiviral expression vector of CaSR, and with Gencode 29 annotations using STAR aligner version 2.6.1a in 2-pass mode.
Raw counts per gene were extracted from the ReadsPerGene.out.tab file generated by STAR aligner.
Genome_build: GRCh38 complemented with additional sequences for the lentiviral expression vector of CaSR
Supplementary_files_format_and_content: Tab-delimited file containing counts per genes for each sample

source_name: HT29GFP + R568

growth_protocol: The cells were cultured in DMEM with 10% FCS, 100 U/ml Pen-Strep, 2mM L-glutamine and 10mM Hepes. Cells were splitted every time they were reacing 80% confluency.

extract_protocol:
Cells were harvested and lysed in TRIZOL and RNA was column purified using RNAmini prep (QIAGEN).
Sequencing libraries were prepared using the NEBNext Poly(A) mRNA Magnetic Isolation Module, the NEBNext UltraTM II Directional RNA Library Prep Kit for Illumina and the NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1) according to manufacturer's protocols (New England Biolabs).
Single-end stranded mRNA-Seq. Pooled libraries were sequenced on a NextSeq500 instrument (Illumina) in 1x75bp single-end sequencing mode.

treatment_protocol: Transfduced cells were treated for 48h either with 0.1% DMSO as untreated control either with 1µM R568.

tag: cell line

value: HT-29 (ATCC HTB-38)

tag: tumor type

value: colorectal adenocarcinoma

tag: passages


title: EK02011: HT29CaSR-GFP + R568

source_name: HT29CaSR-GFP + R568


title: EK02003: HT29GFP + DMSO

source_name: HT29GFP + DMSO

value: DMSO


title: EK02002: HT29GFP + DMSO


title: EK02012: HT29CaSR-GFP + R568


title: EK02008: HT29CaSR-GFP + DMSO

source_name: HT29CaSR-GFP + DMSO


title: EK02006: HT29GFP + R568


title: EK02010: HT29CaSR-GFP + R568


title: EK02007: HT29CaSR-GFP + DMSO


title: H1437 IKKa Wildtype xenograft tumor 1_3

city: Belmont

last: Habiel

state: MA

address: 375 Acorn Park Drive,, Apt. 1416

institute: Cedars-Sinai Medical Center

description:
H1437 IKKa Wt 1_S8_L003
H1437 IKKa Wt 1_L003

data_processing:
Raw Fastq sequencing files were then imported into CLC Biomedical Genomics Workbench version 5.0.1.
The qualities of the samples were assessed and sequences with low quality were trimmed as follows: Quality limit was set to 0.05 and ambiguous limit was set to 2.
Sequences with high quality were then aligned using CLC Biomedical Genomics Workbench using the following parameters: Reference type = Genome annotated with genes and transcripts; reference sequence = homo_sapiens_sequence_hg38; gene track = homo sapiens Ensembl v90 genes; mRNA track = homo sapiens Ensembl v90 mRNA; mismatch cost = 2; insertion cost = 3; deletion cost = 3, length fraction = 0.8; similarity fraction = 0.8; global alignment = no; strand-specific = both; maximum number of hits for a read = 10; count paired reads as two = no and expression value = total counts.
Genome_build: hg38; Ensembl v90 genes
Supplementary_files_format_and_content: counts of each aligned transcript as determined by CLC Biomedical Genomics Bench version 5.0.1.

source_name: H1437 IKKa Wildtype xenograft tumor 1

growth_protocol: IKKa-Ko or WT tumors were isolated from mice and processed for RNA extraction

extract_protocol:
Total cell RNA sample quality and integrity were verified with an Agilent RNA 6000 nano kit or also by quantifying the relative levels of expression of 28S vs. 18S rRNAs by MOPS denaturing agarose gel electrophoresis. RNA-seq libraries were prepared with the Illumina TruSeq RNA v2 kit using 1 μg of total RNA.
Libraries were checked with the Agilent bioanalyzer DNA1000 chip, quantified with the Qubit HS spectrophotometric method and pooled in equimolar amounts for Sequencing. 75 bp Single-End reads were generated with the Illumina NextSeq 500.

tag: host strain

value: NSG (NOD-SCID-IL2Rgamma) mice

value: Skin Xenograft Tumor

tag: cell line source

value: IKKa Wt


title: H1437 IKKa Wildtype xenograft tumor 1_4

description:
H1437 IKKa Wt 1_S8_L004
H1437 IKKa Wt 1_L004


title: H1437 IKKa Wildtype xenograft tumor 3_2

description:
H1437 IKKa Wt 3_S14_L002
H1437 IKKa Wt 3_L002

source_name: H1437 IKKa Wildtype xenograft tumor 3


title: H1437 IKKa Wildtype xenograft tumor 2_3

description:
H1437 IKKa Wt 2_S15_L003
H1437 IKKa Wt 2_L003

source_name: H1437 IKKa Wildtype xenograft tumor 2


title: H1437 IKKa Wildtype xenograft tumor 2_2

description:
H1437 IKKa Wt 2_S15_L002
H1437 IKKa Wt 2_L002


title: H1437 IKKa Wildtype xenograft tumor 2_4

description:
H1437 IKKa Wt 2_S15_L004
H1437 IKKa Wt 2_L004


title: H1437 IKKa Wildtype xenograft tumor 2_1

description:
H1437 IKKa Wt 2_S15_L001
H1437 IKKa Wt 2_L001


title: H1437 IKKa Wildtype xenograft tumor 3_1

description:
H1437 IKKa Wt 3_S14_L001
H1437 IKKa Wt 3_L001


title: H1437 IKKa Wildtype xenograft tumor 1_1

description:
H1437 IKKa Wt 1_S8_L001
H1437 IKKa Wt 1_L001


title: EK02001: HT29GFP + DMSO


title: H1437 IKKa knockout xenograft tumor 3_4

description:
H1437 IKKa Ko 3_S12_L004
H1437 IKKa Ko 3_L004

source_name: H1437 IKKa knockout xenograft tumor 3

value: IKKa Ko


title: H1437 IKKa Wildtype xenograft tumor 3_4

description:
H1437 IKKa Wt 3_S14_L004
H1437 IKKa Wt 3_L004


title: EK02009: HT29CaSR-GFP + DMSO


title: H1437 IKKa knockout xenograft tumor 3_2

description:
H1437 IKKa Ko 3_S12_L002
H1437 IKKa Ko 3_L002


title: EK02005: HT29GFP + R568


title: H1437 IKKa Wildtype xenograft tumor 1_2

description:
H1437 IKKa Wt 1_S8_L002
H1437 IKKa Wt 1_L002


title: H1437 IKKa knockout xenograft tumor 3_1

description:
H1437 IKKa Ko 3_S12_L001
H1437 IKKa Ko 3_L001


title: H1437 IKKa Wildtype xenograft tumor 3_3

description:
H1437 IKKa Wt 3_S14_L003
H1437 IKKa Wt 3_L003


title: H1437 IKKa knockout xenograft tumor 2_4

description:
H1437 IKKa Ko 2_S13_L004
H1437 IKKa Ko 2_L004

source_name: H1437 IKKa knockout xenograft tumor 2


title: H1437 IKKa knockout xenograft tumor 2_2

description:
H1437 IKKa Ko 2_S13_L002
H1437 IKKa Ko 2_L002


title: H1437 IKKa knockout xenograft tumor 1_4

description:
H1437 IKKa Ko 1_S3_L004
H1437 IKKa Ko 1_L004

source_name: H1437 IKKa knockout xenograft tumor 1


title: H1437 IKKa knockout xenograft tumor 1_2

description:
H1437 IKKa Ko 1_S3_L002
H1437 IKKa Ko 1_L002


title: H1437 IKKa knockout xenograft tumor 1_3

description:
H1437 IKKa Ko 1_S3_L003
H1437 IKKa Ko 1_L003


title: H1437 IKKa knockout xenograft tumor 2_3

description:
H1437 IKKa Ko 2_S13_L003
H1437 IKKa Ko 2_L003


title: H1437 IKKa knockout xenograft tumor 3_3

description:
H1437 IKKa Ko 3_S12_L003
H1437 IKKa Ko 3_L003


title: H1299 IKKa Wildtype xenograft tumor 3_4

description:
H1299 IKKa Wt 3_S16_L004
H1299 IKKa Wt 3_L004

source_name: H1299 IKKa Wildtype xenograft tumor 3


title: H1299 IKKa Wildtype xenograft tumor 3_3

description:
H1299 IKKa Wt 3_S16_L003
H1299 IKKa Wt 3_L003


title: H1299 IKKa Wildtype xenograft tumor 2_2

description:
H1299 IKKa Wt 2_S9_L002
H1299 IKKa Wt 2_L002

source_name: H1299 IKKa Wildtype xenograft tumor 2


title: H1299 IKKa Wildtype xenograft tumor 2_1

description:
H1299 IKKa Wt 2_S9_L001
H1299 IKKa Wt 2_L001


title: H1299 IKKa Wildtype xenograft tumor 2_4

description:
H1299 IKKa Wt 2_S9_L004
H1299 IKKa Wt 2_L004


title: H1299 IKKa knockout xenograft tumor 3_2

description:
H1299 IKKa Ko 3_S6_L002
H1299 IKKa Ko 3_L002

source_name: H1299 IKKa knockout xenograft tumor 3


title: H1299 IKKa Wildtype xenograft tumor 3_2

description:
H1299 IKKa Wt 3_S16_L002
H1299 IKKa Wt 3_L002


title: H1299 IKKa knockout xenograft tumor 3_1

description:
H1299 IKKa Ko 3_S6_L001
H1299 IKKa Ko 3_L001


title: H1299 IKKa knockout xenograft tumor 3_3

description:
H1299 IKKa Ko 3_S6_L003
H1299 IKKa Ko 3_L003


title: H1299 IKKa Wildtype xenograft tumor 3_1

description:
H1299 IKKa Wt 3_S16_L001
H1299 IKKa Wt 3_L001


title: H1299 IKKa knockout xenograft tumor 3_4

description:
H1299 IKKa Ko 3_S6_L004
H1299 IKKa Ko 3_L004


title: H1299 IKKa Wildtype xenograft tumor 1_1

description:
H1299 IKKa Wt 1_S10_L001
H1299 IKKa Wt 1_L001

source_name: H1299 IKKa Wildtype xenograft tumor 1


title: H1299 IKKa Wildtype xenograft tumor 1_2

description:
H1299 IKKa Wt 1_S10_L002
H1299 IKKa Wt 1_L002


title: H1299 IKKa knockout xenograft tumor 2_2

description:
H1299 IKKa Ko 2_S7_L002
H1299 IKKa Ko 2_L002

source_name: H1299 IKKa knockout xenograft tumor 2


title: H1299 IKKa knockout xenograft tumor 2_1

description:
H1299 IKKa Ko 2_S7_L001
H1299 IKKa Ko 2_L001


title: H1299 IKKa knockout xenograft tumor 2_3

description:
H1299 IKKa Ko 2_S7_L003
H1299 IKKa Ko 2_L003


title: H1299 IKKa knockout xenograft tumor 2_4

description:
H1299 IKKa Ko 2_S7_L004
H1299 IKKa Ko 2_L004


title: H1437 IKKa knockout xenograft tumor 2_1

description:
H1437 IKKa Ko 2_S13_L001
H1437 IKKa Ko 2_L001


title: H1299 IKKa Wildtype xenograft tumor 2_3

description:
H1299 IKKa Wt 2_S9_L003
H1299 IKKa Wt 2_L003


title: H1299 IKKa Wildtype xenograft tumor 1_3

description:
H1299 IKKa Wt 1_S10_L003
H1299 IKKa Wt 1_L003


title: H1299 IKKa knockout xenograft tumor 1_4

description:
H1299 IKKa Ko 1_S8_L004
H1299 IKKa Ko 1_L004

source_name: H1299 IKKa knockout xenograft tumor 1


title: H1299 IKKa knockout xenograft tumor 1_3

description:
H1299 IKKa Ko 1_S8_L003
H1299 IKKa Ko 1_L003


title: H1299 IKKa knockout xenograft tumor 1_2

description:
H1299 IKKa Ko 1_S8_L002
H1299 IKKa Ko 1_L002


title: KOWT_KO1_nuclear

source_name: Cortex nucleus

value: Male


title: H1299 IKKa Wildtype xenograft tumor 1_4

description:
H1299 IKKa Wt 1_S10_L004
H1299 IKKa Wt 1_L004


title: A549 IKKa Wildtype xenograft tumor 3_2

description:
A549 IKKa Wt 3_S5_L002
A549 IKKa Wt 3_L002

source_name: A549 IKKa Wildtype xenograft tumor 3


title: A549 IKKa Wildtype xenograft tumor 3_3

description:
A549 IKKa Wt 3_S5_L003
A549 IKKa Wt 3_L003


title: A549 IKKa Wildtype xenograft tumor 3_1

description:
A549 IKKa Wt 3_S5_L001
A549 IKKa Wt 3_L001


title: H1299 IKKa knockout xenograft tumor 1_1

description:
H1299 IKKa Ko 1_S8_L001
H1299 IKKa Ko 1_L001


title: A549 IKKa Wildtype xenograft tumor 2_3

description:
A549 IKKa Wt 2_S11_L003
A549 IKKa Wt 2_L003

source_name: A549 IKKa Wildtype xenograft tumor 2


title: A549 IKKa Wildtype xenograft tumor 2_2

description:
A549 IKKa Wt 2_S11_L002
A549 IKKa Wt 2_L002


title: A549 IKKa Wildtype xenograft tumor 1_1

description:
A549 IKKa Wt 1_S7_L001
A549 IKKa Wt 1_L001

source_name: A549 IKKa Wildtype xenograft tumor 1


title: A549 IKKa Wildtype xenograft tumor 2_4

description:
A549 IKKa Wt 2_S11_L004
A549 IKKa Wt 2_L004


title: A549 IKKa Wildtype xenograft tumor 1_4

description:
A549 IKKa Wt 1_S7_L004
A549 IKKa Wt 1_L004


title: A549 IKKa knockout xenograft tumor 3_4

description:
A549 IKKa Ko 3_S2_L004
A549 IKKa Ko 3_L004

source_name: A549 IKKa knockout xenograft tumor 3


title: A549 IKKa Wildtype xenograft tumor 2_1

description:
A549 IKKa Wt 2_S11_L001
A549 IKKa Wt 2_L001


title: A549 IKKa knockout xenograft tumor 3_2

description:
A549 IKKa Ko 3_S2_L002
A549 IKKa Ko 3_L002


title: A549 IKKa Wildtype xenograft tumor 1_3

description:
A549 IKKa Wt 1_S7_L003
A549 IKKa Wt 1_L003


title: A549 IKKa knockout xenograft tumor 3_1

description:
A549 IKKa Ko 3_S2_L001
A549 IKKa Ko 3_L001


title: A549 IKKa knockout xenograft tumor 3_3

description:
A549 IKKa Ko 3_S2_L003
A549 IKKa Ko 3_L003


title: A549 IKKa Wildtype xenograft tumor 1_2

description:
A549 IKKa Wt 1_S7_L002
A549 IKKa Wt 1_L002


title: A549 IKKa knockout xenograft tumor 2_4

description:
A549 IKKa Ko 2_S6_L004
A549 IKKa Ko 2_L004

source_name: A549 IKKa knockout xenograft tumor 2


title: H1437 IKKa knockout xenograft tumor 1_1

description:
H1437 IKKa Ko 1_S3_L001
H1437 IKKa Ko 1_L001


title: A549 IKKa knockout xenograft tumor 2_3

description:
A549 IKKa Ko 2_S6_L003
A549 IKKa Ko 2_L003


title: A549 IKKa knockout xenograft tumor 2_2

description:
A549 IKKa Ko 2_S6_L002
A549 IKKa Ko 2_L002


title: A549 IKKa knockout xenograft tumor 2_1

description:
A549 IKKa Ko 2_S6_L001
A549 IKKa Ko 2_L001


title: A549 IKKa Wildtype xenograft tumor 3_4

description:
A549 IKKa Wt 3_S5_L004
A549 IKKa Wt 3_L004


title: A549 IKKa knockout xenograft tumor 1_2

description:
A549 IKKa Ko 1_S10_L002
A549 IKKa Ko 1_L002

source_name: A549 IKKa knockout xenograft tumor 1


title: XDO137

city: Toronto

first: Ming-Sound

last: Tsao

state: Ontario

address: 101 College St

department: Princess Margaret Cancer Research

country: Canada

institute: University Health Network

data_processing:
Quality filtering and adapter trimming: FASTQC and Trimmomatic (standard parameters)
Classifying reads from xenograft samples: Xenome (standard parameters)
Alignment and Quantification: Salmon (standard parameters)
Genome_build: Human hg19 and Mouse mm10: Xenome
Genome_build: Human GRCh38: Alignment and Quantification by Salmon
Supplementary_files_format_and_content: tab-delimited csv file includes log2 (TPM+1) values for each sample

source_name: organoid

growth_protocol: PDXs were grown in NOD/SCID mice; Organoids were cultured in standard AdDMEMF12 medium with additional supplements

extract_protocol:
Patient tissue and PDX were homogenized in TriZol and organoids were gently lysed in Trizol. RNA was extracted by chloroform and isopropanol precipitation. Illumina TruSeq Stranded mRNA sample preparation kit  (Cat# 20020594) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: organoid

value: lung


title: Patient_344

source_name: patient tumor

value: non-small cell lung cancer (NSCLC) patient tumor tissue


title: A549 IKKa knockout xenograft tumor 1_1

description:
A549 IKKa Ko 1_S10_L001
A549 IKKa Ko 1_L001


title: A549 IKKa knockout xenograft tumor 1_4

description:
A549 IKKa Ko 1_S10_L004
A549 IKKa Ko 1_L004


title: Patient_137


title: A549 IKKa knockout xenograft tumor 1_3

description:
A549 IKKa Ko 1_S10_L003
A549 IKKa Ko 1_L003


title: PDX344

source_name: PDX

value: patient-derived xenograft (PDX)

tag: host mouse strain

value: NOD/SCID


title: LPTO126_org


title: PDX137


title: Patient_LPTO126


title: XDO149


title: Patient_149


title: LPTO85_org


title: PDX149


title: PDX274


title: XDO274


title: PDX4056


title: Patient_274


title: XDO4056_XDO


title: XDO426


title: Patient_426


title: PDX426


title: SLPC54


title: PDO54


title: XDO344


title: Patient_LPTO85


title: mDIV4-2Mg

city: Richardson

first: Theodore

middle: John

last: Price

state: TX

address: 800 W Campbell Rd

department: Behavioral and Brain Sciences

institute: The University of Texas at Dallas

description: Gereau lab cultured DRG

data_processing:
STAR used for read mapping to reference genome and transcriptome
Relative abundances renormalized to 1 million in the set of protein coding genes
Downstream analysis details at doi: https://doi.org/10.1101/766865
Genome_build: Gencode vM16 and GRCm38.p5
Supplementary_files_format_and_content: tab-delimited text file includes TPM values for each sample

source_name: DRG

growth_protocol:
Price lab - All procedures were approved by the Institutional Animal Care and Use Committee of University of Texas at Dallas and were in strict accordance with the US National Institute of Health (NIH) Guide for the Care and Use of Laboratory Animals. Adult C57Bl/6 mice (8-15 weeks of age) were bred in house, and were originally obtained from The Jackson Laboratory. Animals were housed in the University of Texas at Dallas animal facilities on a 12 hour light/dark cycle with access ad libitum to food and water. Male and female C57BL/6 mice (4 week-old, ∼15-20 g; n=3, for each sex) were anesthetized with isoflurane and killed by decapitation. Mice were not perfused prior to removal of DRGs. Lumbar DRGs (L1-L6) from one side of the spine were frozen in RNAlater (Invitrogen) while DRGs from the other side from the same mouse was cultured and then scraped at 4 DIV into RNAlater. L1-L6 DRGs for culturing were dissected and placed in chilled HBSS (Invitrogen) until processed. DRGs were then digested in 1 mg/ml collagenase A (Roche) for 25 min at 37°C then subsequently digested in 1 mg/ml collagenase D for 20 min at 37°C. DRGs were then triturated in 1 mg/ml trypsin inhibitor (Roche), then filtered through a 70 μm cell strainer (Corning). Cells were pelleted then resuspended in DMEM/F12 with GlutaMAX (Thermo Fisher Scientific) containing 10% fetal bovine serum (FBS; Thermo Fisher Scientific), 1% penicillin and streptomycin, 5 ng/mL mouse 2.5S NGF (Millipore), and 3 μg/ml 5-fluorouridine with 7 μg/ml uridine. Cells were distributed evenly across 4 wells using a 24-well plate coated with poly-D-lysine (Becton Dickinson). DRG neurons were maintained in a 37°C incubator containing 5% CO2 with a media change every other day. At 4 DIV, cells were scraped into 500 uL RNAlater and processed for RNA extraction.
Gereau lab - All procedures were approved by the Animal Care and Use Committee of Washington University and in strict accordance with the US National Institute of Health (NIH) Guide for the Care and Use of Laboratory Animals. Adult C57Bl/6 mice (8-15 weeks of age) were bred in house, originally obtained from Jackson Laboratory. Animals were housed in Washington University School of Medicine animal facilities on a 12 hour light/dark cycle with access ad libitum to food and water. The  Male and female C57Bl/6 mice (n=3, for each sex) were deeply anesthetized with isoflurane and quickly decapitated. Mice were not perfused prior to removal of DRGs. From one side, L1-6 DRG were extracted, directly placed into 500μL RNAlater, and stored at -80°C. From the other side, L1-6 DRG were extracted and dissociated in freshly made N-methyl-D-glucamine (NMDG) solution (Valtcheva et al 2016).  DRG were digested in 15U/mL papain (Worthington Biochemical) for 20min at 37°C, washed, and then further digested in 1.5 mg/mL collagenase type 2 (Sigma) for another 20 min at 37°C.  DRG were washed and triturated in DRG media [5% fetal bovine serum (Gibco) and 1% penicillin/streptomycin (Corning) in Neurobasal A medium 1x (Gibco) plus Glutamax (Life Technologies) and B27 (Gibco)].  Final solutions of cells were filtered (40 µm, Fisher) and cultured in DRG media on coverslips coated with poly-D-lysine (Sigma) and rat tail collagen (Sigma).  Cultures were maintained in an incubator at 37°C containing 5% CO2. On 4th DIV (no media changes), cultured coverslips were scraped in 500 μL RNA later and stored at -80°C.

extract_protocol:
Human and mouse DRG tissue/cultured cells were stored in RNAlater and frozen in -80 °C until use. Samples obtained at the Washington University at St Louis were shipped to UT Dallas on dry ice for uniform library preparation. All RNA isolation and sequencing was done in the Price Lab. On the day of use, the frozen tubes were thawed to room temperature. To obtain RNA from tissue samples, the tissue was extracted from RNAlater with ethanol cleaned tweezers and put in 1 mL of QIAzol (QIAGEN Inc.) inside 2 mL tissue homogenizing CKMix tubes (Bertin Instruments). To obtain RNA from cell cultures, cells were spun down to the bottom of the tube by centrifuge at 5000 x g for 10 min. RNAlater was then removed from the tube, and cells were resuspended with 1 mL of QIAzol and transferred to the homogenizing tube. For both tissues and cell cultures, homogenization was performed for 3 x 1 min with Minilys personal homogenizer (Bertin Instruments) at 4 °C. This time course was used to avoid heating during homogenization. RNA extraction was performed with RNeasy Plus Universal Mini Kit (QIAGEN Inc.) with the manufacturer provided protocol. RNA was eluted with 30 µL of RNase free water.
Stranded single end Illumina Truseq total RNA library
Multiplexed libraries were sequenced in a single sequencer run

value: DRG cell culture

value: M


title: mDIV4-4Fg

description: Gereau lab cultured DRG

value: F


title: mDIV4-5Fg

description: Gereau lab cultured DRG


title: mDIV4-3Mg

description: Gereau lab cultured DRG


title: mDIV4-6Fg

description: Gereau lab cultured DRG


title: mDIV4-1Mp

description: Price lab cultured DRG


title: mDIV4-4Fp

description: Price lab cultured DRG


title: mDIV4-5Fp

description: Price lab cultured DRG


title: mDIV4-3Mp

description: Price lab cultured DRG


title: mDIV4-6Fp

description: Price lab cultured DRG


title: mDIV4-2Mp

description: Price lab cultured DRG


title: mDRG-6Fp

description: Price lab intact DRG

value: DRG


title: mDRG-1Mg

description: Gereau lab intact DRG


title: mDRG-2Mg

description: Gereau lab intact DRG


title: mDRG-6Fg

description: Gereau lab intact DRG


title: mDRG-5Fp

description: Price lab intact DRG


title: mDRG-5Fg

description: Gereau lab intact DRG


title: mDRG-3Mg

description: Gereau lab intact DRG


title: mDRG-4Fg

description: Gereau lab intact DRG


title: mDRG-4Fp

description: Price lab intact DRG


title: mDRG-2Mp

description: Price lab intact DRG


title: mDRG-3Mp

description: Price lab intact DRG


title: mDRG-1Mp

description: Price lab intact DRG


title: Mouse IKKa knockout NSCLC tumor 1_4

description:
Mu IKKa KO 1_S13_L001
Mu IKKa KO 1_L004

source_name: Mouse IKKa knockout NSCLC tumor 1

value: Lung NSCLC Tumors

value: IKKa KO


title: Mouse IKKa knockout NSCLC tumor 1_2

description:
Mu IKKa KO 1_S13_L003
Mu IKKa KO 1_L002


title: Mouse IKKa knockout NSCLC tumor 1_3

description:
Mu IKKa KO 1_S13_L002
Mu IKKa KO 1_L003


title: Mouse IKKa knockout NSCLC tumor 1_1

description:
Mu IKKa KO 1_S13_L004
Mu IKKa KO 1_L001


title: mDIV4-1Mg

description: Gereau lab cultured DRG


title: Mouse IKKa knockout NSCLC tumor 2_4

description:
Mu IKKa KO 2_S12_L004
Mu IKKa KO 2_L004

source_name: Mouse IKKa knockout NSCLC tumor 2


title: Mouse IKKa knockout NSCLC tumor 2_3

description:
Mu IKKa KO 2_S12_L003
Mu IKKa KO 2_L003


title: Mouse IKKa knockout NSCLC tumor 2_2

description:
Mu IKKa KO 2_S12_L002
Mu IKKa KO 2_L002


title: Mouse IKKa knockout NSCLC tumor 3_4

description:
Mu IKKa KO 3_S11_L004
Mu IKKa KO 3_L004

source_name: Mouse IKKa knockout NSCLC tumor 3


title: Mouse IKKa knockout NSCLC tumor 3_1

description:
Mu IKKa KO 3_S11_L001
Mu IKKa KO 3_L001


title: Mouse IKKa WildType NSCLC tumor 5_2

description:
Mu IKKa Wt 5_S5_L002
Mu IKKa Wt 5_L002

source_name: Mouse IKKa WildType NSCLC tumor 5


title: Mouse IKKa WildType NSCLC tumor 4_2

description:
Mu IKKa Wt 4_S1_L002
Mu IKKa Wt 4_L003

source_name: Mouse IKKa WildType NSCLC tumor 4


title: Mouse IKKa WildType NSCLC tumor 4_3

description:
Mu IKKa Wt 4_S1_L003
Mu IKKa Wt 4_L004


title: Mouse IKKa WildType NSCLC tumor 4_4

description:
Mu IKKa Wt 4_S1_L004
Mu IKKa Wt 4_L002


title: Mouse IKKa knockout NSCLC tumor 3_3

description:
Mu IKKa KO 3_S11_L003
Mu IKKa KO 3_L003


title: Mouse IKKa WildType NSCLC tumor 5_3

description:
Mu IKKa Wt 5_S5_L003
Mu IKKa Wt 5_L003


title: Mouse IKKa knockout NSCLC tumor 3_2

description:
Mu IKKa KO 3_S11_L002
Mu IKKa KO 3_L002


title: Mouse IKKa knockout NSCLC tumor 2_1

description:
Mu IKKa KO 2_S12_L001
Mu IKKa KO 2_L001


title: Mouse IKKa WildType NSCLC tumor 6_3

description:
Mu IKKa Wt 6_S4_L002
Mu IKKa Wt 6_L003

source_name: Mouse IKKa WildType NSCLC tumor 6


title: Mouse IKKa WildType NSCLC tumor 5_4

description:
Mu IKKa Wt 5_S5_L004
Mu IKKa Wt 5_L004


title: Mouse IKKa WildType NSCLC tumor 5_1

description:
Mu IKKa Wt 5_S5_L001
Mu IKKa Wt 5_L001


title: Mouse IKKa WildType NSCLC tumor 4_1

description:
Mu IKKa Wt 4_S1_L001
Mu IKKa Wt 4_L001


title: Mouse IKKa WildType NSCLC tumor 6_2

description:
Mu IKKa Wt 6_S4_L003
Mu IKKa Wt 6_L002


title: Mouse IKKa WildType NSCLC tumor 6_4

description:
Mu IKKa Wt 6_S4_L001
Mu IKKa Wt 6_L004


title: MeCP2_KO_HiC_rep3

city: Boston

first: Lisa

middle: D.

last: Boxer

address: 220 Longwood Ave., Goldenson Bldg Rm 405

department: Neurobiology

data_processing:
Paired end reads were aligned against the mm10 genome using BWA.
PCR duplicates, low mapping quality and unligated reads were removed using Juicer, version 1.5.6 (Durand, Shamim, et al Cell Systems 2016).
Read coordinates were then imported into Misha mm10 database (https://tanaylab.bitbucket.io/shaman/articles/import.html), excluding reads with MAPQ<30 and reads mapping on the same fragment.
Observed contacts were then further normalised and processed using Shaman (https://doi.org/10.1101/187203)
Genome_build: mm10
Supplementary_files_format_and_content: .txt.gz   Processed files are in the “long format” according to the juicer pipeline (https://github.com/aidenlab/juicer/wiki/Pre). Briefly, this is a whitespace separated file that contains, on each line: <str1> <chr1> <pos1> <frag1> <str2> <chr2> <pos2> <frag2> <mapq1> <cigar1> <sequence1> <mapq2> <cigar2> <sequence2> <readname1> <readname2>. str = strand (0 for forward, anything else for reverse); chr = chromosome (must be a chromosome in the genome); pos = position; frag = restriction site fragment; mapq = mapping quality score; cigar = cigar string as reported by aligner; sequence = DNA sequence. This file can be used as input for either Juicebox (Durand, Robinson, et al Cell Systems 2016) or Shaman (https://doi.org/10.1101/187203) based analysis.

source_name: Forebrain tissue

extract_protocol:
Forebrain (cortex and hippocampus) was dissected from 8-week-old MeCP2 KO and WT mice and flash frozen. In situ Hi-C was performed as described in (Rao et al., 2014) with minor modifications. Tissue was homogenized in 1% formaldehyde in PBS and rotated for 10 minutes at room temperature. Cross-linking was quenched with 125 mM glycine for 5 minutes at room temperature. Tissue was pelleted by spinning at 500 g for 5 minutes at 4°C, washed once with PBS, then spun again at 500 g for 5 minutes at 4°C. Cells were lysed by resuspending in 500 μL Hi-C lysis buffer (10 mM Tris pH 8.0, 10 mM NaCl, 0.2% Igepal CA630) with protease inhibitors (Sigma P8340), incubated on ice for 15 minutes, then spun at 2500 g for 5 minutes at 4°C. Pelleted nuclei were washed with Hi-C lysis buffer, then spun at 2500 g for 5 minutes at 4°C. Nuclei were resuspended in 50 μL 0.5% sodium dodecyl sulfate (SDS) and incubated at 62°C for 7.5 minutes. After heating, 115 μL of water and 25 μL of 10% Triton X-100 were added to quench the SDS, and samples were incubated at 37°C for 15 minutes. Restriction digest was performed by adding 25 μL of 10X NEB Buffer 2 and 100 U of MboI (NEB R0147) and rotating 16 hours at 37°C. Samples were incubated at 62°C for 20 minutes to inactivate MboI. To fill in restriction fragment overhangs and mark DNA ends with biotin, 50 μL of fill-in master mix was added (37.5 μL of 0.4 mM biotin-14-dATP, 1.5 μL of 10mM dCTP, 15 μL of 10mM dGTP, 1.5 μL of 10mM dTTP, and 8 μL 5U/μL DNA Polymerase I, Large (Klenow) Fragment (NEB, M0210)), and samples were rotated for 75 minutes at 37°C. 900 μL of Ligation master mix was added (669 μL of water, 120 μL of 10X NEB T4 DNA ligase buffer (NEB, B0202), 100 μL 10% Triton X-100, 6 μl 20 mg/mL Bovine Serum Albumin, and 5 μL of 400 U/μL T4 DNA Ligase (NEB, M0202)), and samples were rotated at room temperature for 4 hours. Protein was degraded by adding 50 μL 20 mg/mL proteinase K (NEB, P8102) and 120 μL of 10% SDS and incubating at 55°C for 30 minutes on a Thermomixer at 350 rpm. 130 μL of 5M NaCl was added and samples were incubated at 68°C for 16 hours to reverse cross-links. DNA was purified by adding 1.6X volumes of ethanol and 0.1X volumes of 3M sodium acetate, pH 5.2 and incubated at -80°C for 15 minutes. Samples were spun at 17,720 g for 15 minutes at 4°C, washed with 70% ethanol, and spun at 17,720 g for 5 minutes at 4°C. Pellet was resuspended in 130 uL 1X Tris buffer (10 mM Tris-HCl, pH 8) and incubated at 37°C to fully dissolve DNA.
To make biotinylated DNA suitable for high-throughput sequencing, DNA was sheared with a Covaris M220 (Peak incident power: 50, Duty factor: 10%, Cycles per burst: 200, Treatment time: 70 seconds). DNA fragments in the range of 300-500 bp were selected using AMPure XP beads. 150 μL of 10 mg/mL MyOne Streptavidin T1 beads were washed with 400 μL 1X Tween Washing Buffer (TWB: 5 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 1M NaCl, 0.05% Tween 20). Beads were resuspended in 300 μL 2X Binding Buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 2M NaCl), added to samples, and rotated for 15 minutes at room temperature. Beads were separated on a magnet and washed twice with 600 μL TWB, incubating at 55°C with mixing at 350 rpm for 2 minutes on a Thermomixer, and transferring to a new tube with each wash. Beads were washed once with 100ul 1X NEB T4 DNA ligase buffer, then resuspended in 100 μl of master mix (88ul 1X NEB T4 DNA ligase buffer, 2 ul 25 mM dNTP mix, 5 ul 10U/ul NEB T4 PNK (NEB, M0201), 4 ul of 3U/ul NEB T4 DNA polymerase I (NEB, M0203), and 1 ul of 5U/ul NEB DNA polymerase I, Large (Klenow) Fragment (NEB, M0210)), and incubated at room temperature for 30 minutes. Beads were washed twice with TWB as described above, washed once with 100 ul 1X NEBuffer 2, and resuspended in 100ul dATP attachment master mix (90ul 1X NEBuffer 2, 5ul 10mM dATP, and 5ul of 5U/ul NEB Klenow exo minus (NEB, M0212)), and incubated at 37°C for 30 minutes. Beads were washed twice with TWB as described above and washed once with 100ul 1X Quick ligation reaction buffer (NEB, B6058). Beads were resuspended in 50ul of 1X NEB Quick ligation reaction buffer, and 2ul NEB DNA Quick ligase (NEB, M2200) and 3 ul of NEBNext adapter (NEB E7335) diluted 1:10 in 10mM Tris pH 7.5 were added, and incubated at room temperature for 15 minutes. Beads were washed twice with TWB as described above, and washed once with 100ul 1X Tris buffer. Beads were resuspended in 20ul 1X Tris buffer and boiled at 98°C for 10 minutes to elute DNA off beads. Hi-C libraries were amplified by adding to 17 ul DNA: 25 ul NEBNext Q5 Hot Start HiFi PCR Master Mix (M0543), 3 ul NEBNext USER Enzyme (M5505), 2.5 ul 10uM Index (i7) primer, and 2.5ul Universal (i5) primer (E7335), and amplified for 8 cycles. Libraries were purified with AMPure beads (2 purifications with 0.7X beads)

value: 8 weeks

tag: gender

value: KO


title: MeCP2_KO_HiC_rep2


title: MeCP2_KO_HiC_rep1


title: MeCP2_WT_HiC_rep2

value: WT


title: Mouse IKKa WildType NSCLC tumor 6_1

description:
Mu IKKa Wt 6_S4_L004
Mu IKKa Wt 6_L001

value: IKKa Wt


title: MeCP2_KO_input_R2

data_processing:
Sequencing reads were trimmed with Trimmomatic (v0.36) to remove adaptors and low quality sequence (settings: LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:50).
Trimmed reads were mapped to the mm10 genome with Bowtie2 (v2.2.9) with default parameters.
PCR duplicate reads were removed with Samtools (v0.1.19) rmdup.
Reads were extended to 250 bp (to approximate fragment length) with UCSC tools bedextendranges.
For each ChIP antibody, reads for each sample were randomly down-sampled to equal numbers using the GNU shuf utility.
ChIP-seq reads were quantified in the genomic regions specified in figure legends using Bedtools map (v2.26).
Genome_build: mm10
Supplementary_files_format_and_content: Tables of raw ChIP read counts in either full gene bodies (transcription start site (TSS) to transcription termination site (TTS) of longest isoform), gene bodies excluding the first 3kb (TSS +3kb to TTS), or TSS (TSS -1kb to +1kb). For YY1 ChIP, file contains position of YY1 motifs in YY1 peaks.

extract_protocol:
Forebrain (cortex and hippocampus) was dissected from 8-to-12-week-old male mice and flash frozen. Tissue was homogenized in 1% formaldehyde and cross-linked for 10 minutes at room temperature. Cross-linking was quenched with 125 mM glycine for 5 minutes at room temperature. Tissue was pelleted by spinning at 500 g for 5 minutes at 4°C, washed once with PBS, then spun again at 500 g for 5 minutes at 4°C. Cells were lysed by resuspending in L1 buffer (50 mM Hepes pH 7.5, 140mM NaCl, 1 mM EDTA pH 8, 1 mM EGTA pH 8, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, protease inhibitors) and rotating at 4°C for 10 minutes, then spun at 500 g for 5 minutes at 4°C. Nuclei were washed for 10 minutes at 4°C in L2 buffer (10 mM Tris pH 8, 200 mM NaCl, protease inhibitors), then spun at 500 g for 5 minutes at 4°C. Nuclei were resuspended in LB3 buffer (10 mM Tris pH 8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-Lauroylsarcosine, protease inhibitors), and sonicated in a Diagenode Bioruptor (High Power, 60 cycles, 30 seconds on/45 seconds off). Insoluble material was removed by spinning at 16,000 g for 10 minutes at 4°C, and Triton X-100 was added to soluble chromatin at a final concentration of 1%. Chromatin was pre-cleared for two hours with Protein A (for rabbit antibodies) or Protein G (for mouse antibodies) Dynabeads, then incubated with Protein A or Protein G Dynabeads conjugated to antibodies overnight at 4°C. Antibodies used were: H3K27ac (Abcam ab4729), H3K36me3 (Abcam ab9050), H4K12ac (Millipore 07-595), H3K9ac (Millipore 06-942), H3K79me2 (Abcam ab3594), Pol II (Abcam ab817), Pol II Ser5p (Millipore 04-1572), and MeCP2 Ab1 and pre-immune serum (Chen et al., 2003), and MeCP2 Ab2 (Sigma M6818). Beads were washed twice with Low Salt Buffer (20 mM Tris pH 8, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), twice with High Salt Buffer (20 mM Tris pH 8, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), twice with LiCl Wash Buffer (10 mM Tris pH 8, 1 mM EDTA, 1% NP-40, 250 mM LiCl, 1% sodium deoxycholate) and once with TE Buffer (50 mM Tris pH 8, 10 mM EDTA) at 4°C. Chromatin was eluted off beads by incubating in TE Buffer with 1% SDS at 65°C for one hour, and crosslinks were reversed by incubating overnight at 65°C. Chromatin was treated with RNase A for 30 minutes at 37°C and Proteinase K for 2 hours at 55°C. DNA was phenol-chloroform extracted and purified with the Qiagen PCR purification kit.
Libraries were generated using the NuGEN Ovation Ultralow System V2 following manufacturer instructions.

tag: chip antibody


title: MeCP2_KO_input_R1

tag: strain


title: MeCP2_KO_IgG_ChIPseq_R2

value: Pre-immune serum (Chen et al., 2003)


title: MeCP2_WT_input_R1

value: Male


title: MeCP2_WT_input_R2


title: MeCP2_KO_IgG_ChIPseq_R1


title: MeCP2_WT_HiC_rep3


title: MeCP2_WT_IgG_ChIPseq_R1


title: R306C_1wk_whole_cell_RNA_rep10

data_processing:
Reads were trimmed with Trimmomatic (v0.36) to remove Illumina adaptors and low quality sequence (settings: LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:50).
Trimmed reads were mapped to the mm10 Refseq transcriptome and genome using STAR (v2.5.2b) with --outFilterMismatchNoverReadLmax 0.04.
For whole-cell RNA-seq, reads were counted in all exons for each gene using Subread featureCounts (v1.6.0) with default parameters (reversely stranded, multi-mapping reads not counted, multi-overlapping reads not counted). For nuclear and chromatin-associated RNA-seq, reads were counted in the full gene body (TSS to TTS of longest isoform, in order to include intronic reads) using Subread featureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: Table of raw read counts for exons or gene bodies for all genes.

extract_protocol:
Forebrain (cortex and hippocampus) was dissected from 10 8-week-old male MeCP2 knock-out and 10 wild-type littermate controls, 10 8-to-12-week-old male R306C and 10 WT littermate controls, and 10 1-week-old male R306C and 10 WT littermate controls and flash frozen. Tissue was removed from dry ice and placed directly into a dounce with 5 mL of Homogenization buffer (HB: 250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine KOH pH 7.8, 0.04% BSA, 5 µg/mL Actinomycin D, and RNAsin (Promega)). After 10 strokes with the tight pestle, a 5% Igepal (Sigma) solution in HB was added to a final concentration of 0.32%, followed by five additional strokes with the tight pestle. At this point, 200 μL of lysate was pipetted into a tube with 600 µL Trizol LS (Invitrogen) as the “whole cell” sample. The remaining lysate was filtered first through a 40 μm cell strainer and then through a 20 μm Celltrics filter. Lysate was diluted 1:2 in HB to dilute Igepal to 0.16%, then centrifuged at 500 g for 5 minutes at 4°C. The nuclear pellet was washed twice with 1 mL HB by resuspending and centrifuging at 500 g for 5 minutes at 4°C. Nuclei were resuspended in 1mL HB and 200μL was pipetted into a separate tube, spun at 500 g for 5 minutes at 4°C, and the pellet was resuspended in Trizol as the “nuclear fraction”. The remaining 800 μL was spun at 500 g for 5 minutes at 4°C, then resuspended in 200 μL Glycerol buffer (20 mM Tris pH 8, 75 mM NaCl, 0.5 mM EDTA, 50% glycerol, 0.85 mM DTT). 200 μL of Nuclear lysis buffer (1% Igepal, 20 mM Hepes pH 7.5, 300 mM NaCl, 0.2 mM EDTA) was added and nuclei were resuspended, vortexed, and incubated at 4°C for 5 minutes. Chromatin was spun at 16,000 g for 10 minutes at 4°C, and the pellet was resuspended in 800 μL Trizol and homogenized to solubilize. For Dnmt3a cKO mice, visual cortex was dissected and homogenized in Trizol. For all samples, total RNA was chloroform extracted and purified with the Qiagen RNeasy Micro Kit with on-column DNase treatment.
RNA-seq libraries were generated with the NEBNext Ultra Directional Library Prep Kit with rRNA depletion.

value: 1 week

tag: cellular fraction

value: Whole-cell


title: MeCP2_KO_MeCP2_Ab1_ChIPseq_R1

tag: genotype

value: MeCP2 (Chen et al., 2003)


title: MeCP2_KO_MeCP2_Ab1_ChIPseq_R2


title: MeCP2_WT_MeCP2_Ab2_ChIPseq_R2

value: MeCP2 (Sigma M6818)


title: MeCP2_WT_MeCP2_Ab2_ChIPseq_R1


title: R306C_1wk_whole_cell_RNA_rep9


title: MeCP2_WT_MeCP2_Ab1_ChIPseq_R1


title: MeCP2_KO_MeCP2_Ab2_ChIPseq_R2


title: R306C_1wk_whole_cell_RNA_rep4


title: R306C_1wk_whole_cell_RNA_rep6


title: R306C_1wk_whole_cell_RNA_rep7


title: R306C_1wk_whole_cell_RNA_rep5


title: R306C_1wk_whole_cell_RNA_rep3


title: WT_1wk_whole_cell_RNA_rep9


title: WT_1wk_whole_cell_RNA_rep10


title: R306C_1wk_whole_cell_RNA_rep2


title: R306C_1wk_whole_cell_RNA_rep8


title: MeCP2_WT_IgG_ChIPseq_R2


title: WT_1wk_whole_cell_RNA_rep6


title: WT_1wk_whole_cell_RNA_rep7


title: WT_1wk_whole_cell_RNA_rep5


title: WT_1wk_whole_cell_RNA_rep4


title: WT_1wk_whole_cell_RNA_rep3


title: MeCP2_WT_MeCP2_Ab1_ChIPseq_R2


title: WT_1wk_whole_cell_RNA_rep2


title: WT_1wk_whole_cell_RNA_rep1


title: ATAC_OCT4-AID_IAA_10h_2

city: Lausanne

middle: Michael

last: Suter

address: EPFL SV-IN Station 19

department: Institute of Bioengineering

country: Switzerland

institute: École polytechnique fédérale de Lausanne

data_processing:
All sequencing libraries were aligned to the mm10 Mus musculus genome (GRCm38) with STAR 2.6.1c (Dobin et al., 2013) and duplicate reads were removed using Picard (Broad Institute)
Reads not mapping to chromosomes 1-19, X, or Y were removed
Peaks were called with MACS 2.1.1.20160309 (Zhang et al., 2008) with settings ‘-f BAMPE -g mm’
Peaks from all doxycycline-treated and cell cycle phase-sorted samples were merged using BEDTools (Quinlan and Hall, 2010)
Replicate bam files were merged using SAMTools (Li et al., 2009) and converted to bigWig files using the deepTools 3.1.3 (Ramírez et al., 2016) function bamCoverage with settings ‘--normalizeUsingRPKM’
Genome_build: mm10
Supplementary_files_format_and_content: .bw, OCT4-AID_mergepeaks.bed, OCT4-AID_DE.xlsx, OCT4-AID_timepoints_DE.xlsx contains DE values obtained from limma in acessible regions and features overlapping these regions. OCT4-AID_timepoints_normalizedreads.xlsx contains mean values of normalized reads for each time point of treatment in different clusters of loci

source_name: mouse ES cells

growth_protocol: Cells were routinely cultured on dishes coated with 0.1% gelatin type B in GMEM supplemented with 10% ES-cell qualified fetal bovine serum, nonessential amino acids, 2mM L-glutamine, sodium pyruvate, 100μM 2-mercaptoethanol, penicillin and streptomycin, homemade leukemia inhibitory factor (LIF), CHIR99021 at 3μM and PD184352 at 0.8μM.

extract_protocol:
Cells were pelleted and washed with 1X ice cold PBS at 800g for 5 min. Cells were gently resuspended in 50 μl of ice-cold ATAC lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40), and immediately pelleted at 800g for 10 min at 4°C. To transpose open chromatin regions, cells were resuspended in 50 μl of transposition reaction mix containing 0.5 μM of Tn5 transposase (in-house prepared) in TAPS-DMF buffer (10 mM TAPS-NaOH, 5 mM Mgcl2, 10% DMF) and incubated at 37°C for 30 min. The transposed DNA was purified using a DNA purification kit and eluted in 12 μl of water.
A 65 μl PCR reaction was setup with 10 μl of transposed DNA, 0.5 μM of forward primer Ad1_noMX, 0.5 μM of multiplexing reverse primer Ad2.x (Buenrostro et al. 2013), 0.6x SYBR Green I, and 1x PCR Master Mix. The samples were thermocycled at 72°C for 5 minutes, 98°C for 30 s, followed by 12 cycles of 98°C for 10 s, 63°C for 30 s and 72°C for 1 min. The amplified ATAC libraries were purified using a DNA purification kit and size selected using Agencourt AMPure beads (0.55X unbound fraction followed by 1.2X bound fraction).

treatment_protocol: Cells were treated with 1 ug/ml doxycycline for 24 hours prior to treatment with 500 nM IAA or not according to the sample description

tag: treatment

value: 34h dox 10h IAA

tag: cell cycle phase

value: unsorted

tag: expression construct

value: YPet-MD


title: R306C_1wk_whole_cell_RNA_rep1

tag: age


title: ATAC_OCT4-AID_IAA_4h_2

value: 34h dox 4h IAA


title: ATAC_OCT4-AID_IAA_3h_2

value: 34h dox 3h IAA


title: ATAC_OCT4-AID_IAA_2h_2

value: 34h dox 2h IAA


title: ATAC_OCT4-AID_untreated_2

value: 34h dox


title: ATAC_OCT4-AID_IAA_10h_1


title: ATAC_OCT4-AID_IAA_3h_1


title: WT_1wk_whole_cell_RNA_rep8


title: ATAC_OCT4-AID_IAA_30m_1

value: 34h dox 30m IAA


title: ATAC_OCT4-AID_IAA_4h_1


title: ATAC_OCT4-AID_IAA_2h_1


title: ATAC_OCT4-AID_IAA_6h_1

value: 34h dox 6h IAA


title: ATAC_OCT4-AID_IAA_1h_1

value: 34h dox 1h IAA


title: ATAC_OCT4-AID_controlwash_SG2_2

value: 31h dox washout 4.5h

value: Late S/G2


title: MeCP2_KO_MeCP2_Ab2_ChIPseq_R1

value: 8 weeks

value: Male

value: KO


title: ATAC_OCT4-AID_untreated_1


title: ATAC_OCT4-AID_controlwash_S_2

value: S


title: ATAC_OCT4-AID_IAAwash_LG1_2

value: 31h dox 2.5h IAA washout 4.5h

value: Late G1


title: ATAC_OCT4-AID_IAAwash_SG2_2


title: ATAC_OCT4-AID_controlwash_EG1_2

value: Early G1


title: ATAC_OCT4-AID_controlwash_LG1_2

value: YPet-MD


title: ATAC_OCT4-AID_IAAwash_EG1_2


title: ATAC_OCT4-AID_IAA_6h_2

value: unsorted


title: ATAC_OCT4-AID_IAA_1h_2


title: ATAC_OCT4-AID_controlwash_S_1


title: ATAC_OCT4-AID_IAA_30m_2


title: ATAC_OCT4-AID_controlwash_SG2_1


title: ATAC_OCT4-AID_controlwash_LG1_1


title: ATAC_OCT4-AID_controlwash_EG1_1


title: ATAC_OCT4-AID_IAAwash_SG2_1


title: ATAC_OCT4-AID_IAAwash_LG1_1


title: ATAC_OCT4-AID_IAAwash_S_1


title: ATAC_OCT4-AID_SG2_ctrl_3

value: 26h dox


title: ATAC_OCT4-AID_S_ctrl_3


title: ATAC_OCT4-AID_LateG1_ctrl_3


title: MeCP2_WT_HiC_rep1

value: WT


title: ATAC_OCT4-AID_EarlyG1_ctrl_3


title: ATAC_OCT4-AID_S_ctrl_2


title: ATAC_OCT4-AID_IAAwash_S_2


title: ATAC_OCT4-AID_LateG1_IAA_3

value: 26h dox 2h IAA


title: ATAC_OCT4-AID_EarlyG1_IAA_3


title: ATAC_OCT4-AID_LateG1_ctrl_2


title: ATAC_OCT4-AID_S_IAA_2


title: ATAC_OCT4-AID_LateG1_IAA_2


title: ATAC_OCT4-AID_EarlyG1_IAA_2


title: ATAC_OCT4-AID_LateG1_ctrl_1


title: ATAC_OCT4-AID_S_ctrl_1


title: ATAC_OCT4-AID_SG2_ctrl_1


title: ATAC_OCT4-AID_EarlyG1_ctrl_1


title: ATAC_OCT4-AID_S_IAA_1


title: ATAC_OCT4-AID_SG2_IAA_1


title: ATAC_OCT4-AID_LateG1_IAA_1


title: ATAC_OCT4-AID_EarlyG1_IAA_1


title: ATAC_OCT4-AID_S_IAA_3


title: ATAC_OCT4-AID_IAAwash_EG1_1


title: ChIP_MD*-OCT4_SG2_H3K27ac_2

data_processing:
All sequencing libraries were aligned to the mm10 Mus musculus genome (GRCm38) with STAR 2.6.1c (Dobin et al., 2013) and duplicate reads were removed using Picard (Broad Institute)
Reads not mapping to chromosomes 1-19, X, or Y were removed
Replicate bam files were merged using SAMTools (Li et al., 2009) and converted to bigWig files using the deepTools 3.1.3 (Ramírez et al., 2016) function bamCoverage with settings ‘--normalizeUsingRPKM’
Genome_build: mm10
Supplementary_files_format_and_content: .bw

growth_protocol: Cells were routinely cultured on dishes coated with 0.1% gelatin type B in GMEM supplemented with 10% ES-cell qualified fetal bovine serum, nonessential amino acids, 2mM L-glutamine, sodium pyruvate, 100μM 2-mercaptoethanol, penicillin and streptomycin, homemade leukemia inhibitory factor (LIF), CHIR99021 at 3μM and PD184352 at 0.8μM

extract_protocol:
Roughly 10 million cells per sample were collected after trypsinization and fixed with 2 mM disuccinimidyl glutarate (Thermo Fisher Scientific #20593) in PBS for 50 minutes at room temperature, spun down at 600g for 5 minutes and washed once with PBS. Cells were then treated with 1% formaldehyde (Axon Lab #A0877,0500) for 10 minutes at room temperature and quenched with 200mM Tris-HCl pH 8.0 for 10 minutes, washed with PBS and spun down. For ZHBTc4 YPet-MD SNAP-MD-OCT4 and SNAP-MD*-OCT4 cells, cells were subsequently resuspended in cold PBS with 1% FBS and at least 500’000 cells per cell cycle phase were sorted. Fixed cell pellets were kept on ice and resuspended in LB1 (50mM HEPES-KOH pH 7.4, 140mM NaCl, 1 mM EDTA, 0.5mM EGTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100), incubated 10 min at 4°C, spun down at 1700g, and resuspended in LB1 a second time, spun down and resuspended in LB2 (10mM Tris-HCl pH 8.0, 200mM NaCl, 1 mM EDTA, 0.5mM EGTA), incubated for 10 min at 4°C, spun down and washed without disturbing the pellet three times with SDS shearing buffer (10mM Tris-HCl pH 8.0, 1mM EDTA, 0.15% SDS) and finally resuspended in SDS shearing buffer. All buffers contained Protease Inhibtor Cocktail (Sigma #P8340-1ML) at 1:100 dilution. Chromatin was sonicated for 20 min at 5% duty cycle, 140 W, 200 cycles on a Covaris E220 focused ultrasonicator. Sonicated chromatin was equilibrated to 1% Triton X-100 and 150 mM NaCl and incubated with each antibody overnight at 4°C. Antibodies used were anti-BRG1 (Abcam #ab110641) at 5 μg per 10 million cells, anti-OCT4 (Cell Signaling Technology #5677S) at 20 μl per 10 million cells, and anti-H3K27ac (Abcam #ab4729) at 2 μg/25 μg chromatin. Protein G Dynabeads (Thermo Fisher Scientific #10003D) were blocked with 5 mg/ml BSA in PBS, added to chromatin, and incubated at 4°C for 3 hours. Beads were washed twice with Low Salt wash buffer (10mM Tris-HCl pH 8.0, 150mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.15% SDS, 1 mM PMSF), once with High Salt wash buffer (10mM Tris-HCl pH 8.0, 500mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.15% SDS, 1 mM PMSF), once with LiCl wash buffer (10mM Tris-HCl pH 8.0, 1mM EDTA, 0.5mM EGTA, 250mM LiCl, 1% NP40, 1% sodium deoxycholate, 1mM PMSF), and finally with 1X TE (10 mM Tris pH 8.0, 1 mM EDTA) before being resuspended in ChIP Elution buffer (10 mM Tris pH 8.0, 1 mM EDTA, 1% SDS, 150 mM NaCl) with 400 ng/μl Proteinase K (Qiagen #19131) and reverse-crosslinked overnight at 65°C. DNA was purified using a MinElute PCR purification kit (Qiagen #28004)
Libraries were prepared with NEBNext Ultra II DNA Library Prep Kit (NEB #E7645S) kit with insert size selection of 250 bp

treatment_protocol: Cells were treated with 1 ug/ml doxycycline for 40 hours and stained with 50 uM Hoechst33342

value: Anti-H3K27ac (Abcam #ab4729)


title: ChIP_MD*-OCT4_S_H3K27ac_2


title: ATAC_OCT4-AID_SG2_IAA_3


title: ChIP_MD*-OCT4_EG1_H3K27ac_2


title: ChIP_MD-OCT4_SG2_H3K27ac_2


title: ChIP_MD*-OCT4_SG2_H3K27ac_1


title: ChIP_MD-OCT4_S_H3K27ac_2


title: ATAC_OCT4-AID_EarlyG1_ctrl_2


title: ChIP_MD-OCT4_EG1_H3K27ac_2


title: ChIP_MD-OCT4_LG1_H3K27ac_2


title: ChIP_MD*-OCT4_LG1_H3K27ac_1


title: ChIP_MD*-OCT4_EG1_H3K27ac_1


title: ChIP_MD-OCT4_S_H3K27ac_1


title: ChIP_MD-OCT4_SG2_H3K27ac_1


title: ATAC_MD*-OCT4_noDOX_2

data_processing:
All sequencing libraries were aligned to the mm10 Mus musculus genome (GRCm38) with STAR 2.6.1c (Dobin et al., 2013) and duplicate reads were removed using Picard (Broad Institute)
Reads not mapping to chromosomes 1-19, X, or Y were removed
Peaks were called with MACS 2.1.1.20160309 (Zhang et al., 2008) with settings ‘-f BAMPE -g mm’
Peaks from all doxycycline-treated and cell cycle phase-sorted samples were merged using BEDTools (Quinlan and Hall, 2010)
Replicate bam files were merged using SAMTools (Li et al., 2009) and converted to bigWig files using the deepTools 3.1.3 (Ramírez et al., 2016) function bamCoverage with settings ‘--normalizeUsingRPKM’
Genome_build: mm10
Supplementary_files_format_and_content: .bw, MD-OCT4_mergepeaks.bed, MD-OCT4_DE.xlsx file contains DE values obtained from limma in accessible regions and features overlapping these regions

extract_protocol:
Cells were pelleted and washed with 1X ice cold PBS at 800g for 5 min. Cells were gently resuspended in 50 μl of ice-cold ATAC lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40), and immediately pelleted at 800g for 10 min at 4°C. To transpose open chromatin regions, cells were resuspended in 50 μl of transposition reaction mix containing 0.5 μM of Tn5 transposase (in-house prepared) in TAPS-DMF buffer (10 mM TAPS-NaOH, 5 mM Mgcl2, 10% DMF) and incubated at 37°C for 30 min. The transposed DNA was purified using a DNA purification kit and eluted in 10 μl of water
A 65 μl PCR reaction was setup with 10 μl of transposed DNA, 0.5 μM of forward primer Ad1_noMX, 0.5 μM of multiplexing reverse primer Ad2.x (Buenrostro et al. 2013), 0.6x SYBR Green I, and 1x PCR Master Mix. The samples were thermocycled at 72°C for 5 minutes, 98°C for 30 s, followed by 12 cycles of 98°C for 10 s, 63°C for 30 s and 72°C for 1 min. The amplified ATAC libraries were purified using a DNA purification kit and size selected using Agencourt AMPure beads (0.55X unbound fraction followed by 1.2X bound fraction)

value: untreated


title: ChIP_MD-OCT4_EG1_H3K27ac_1


title: ATAC_MD*-OCT4_EG1_2

value: Dox 40 hours


title: ChIP_MD*-OCT4_LG1_H3K27ac_2


title: ATAC_MD*-OCT4_SG2_2


title: ATAC_MD-OCT4_noDOX_2


title: ATAC_MD*-OCT4_noDOX_1


title: ATAC_MD*-OCT4_S_2


title: ATAC_MD-OCT4_noDOX_1


title: ATAC_MD*-OCT4_LG1_2


title: ATAC_MD-OCT4_SG2_2


title: ATAC_MD-OCT4_S_2


title: ATAC_MD*-OCT4_SG2_1


title: ATAC_MD-OCT4_LG1_2


title: ATAC_MD*-OCT4_EG1_1


title: ChIP_MD*-OCT4_S_H3K27ac_1


title: ATAC_MD-OCT4_EG1_2


title: ATAC_MD*-OCT4_S_1


title: ATAC_MD*-OCT4_LG1_1


title: ChIP_MD-OCT4_LG1_H3K27ac_1


title: ATAC_MD-OCT4_SG2_1


title: ATAC_MD-OCT4_LG1_1


title: ATAC_MD-OCT4_EG1_1


title: ATAC_MD-OCT4_S_1


title: ChIP_H3K27ac_OCT4OFF_S2iL_1

data_processing:
All sequencing libraries were aligned to the mm10 Mus musculus genome (GRCm38) with STAR 2.6.1c (Dobin et al., 2013) and duplicate reads were removed using Picard (Broad Institute)
Reads not mapping to chromosomes 1-19, X, or Y were removed
Peaks were called with MACS 2.1.1.20160309 (Zhang et al., 2008) with settings ‘-f BAMPE -g mm’
Peaks from replicates were merged with BEDTools (Quinlan and Hall, 2010)
Replicate bam files were merged using SAMTools (Li et al., 2009) and converted to bigWig files using the deepTools 3.1.3 (Ramírez et al., 2016) function bamCoverage with settings ‘--normalizeUsingRPKM’
Genome_build: mm10
Supplementary_files_format_and_content: .bw, OCT4_2TS22C_ChIP_merge.bed

treatment_protocol: Cells were treated with 1 ug/ml doxycycline or left untreated for 26h (2TS22C) or 24h (ZHBTc4)

value: Dox 24 hours


title: ChIP_H3K27ac_OCT4ON_S2iL_1

value: Untreated 24 hours


title: ChIP_H3K27ac_OCT4OFF_S2iL_2


title: ChIP_H3K27ac_SOX2OFF_26h_1

value: Dox 26 hours


title: ChIP_H3K27ac_SOX2ON_26h_2

value: Untreated 26 hours


title: ChIP_H3K27ac_SOX2OFF_26h_2


title: ChIP_BRG1_SOX2ON_26h_2

value: Anti-BRG1 (Abcam #ab110641)


title: ChIP_OCT4_SOX2OFF_26h_1

value: Anti-OCT4 (CST #5677S)


title: ChIP_H3K27ac_SOX2ON_26h_1


title: ChIP_BRG1_SOX2OFF_26h_2


title: ChIP_BRG1_SOX2OFF_26h_1


title: ATAC_SOX2OFF_40h_2

data_processing:
All sequencing libraries were aligned to the mm10 Mus musculus genome (GRCm38) with STAR 2.6.1c (Dobin et al., 2013) and duplicate reads were removed using Picard (Broad Institute)
Reads not mapping to chromosomes 1-19, X, or Y were removed
Peaks were called with MACS 2.1.1.20160309 (Zhang et al., 2008) with settings ‘-f BAMPE -g mm’
Peaks from ZHBTc4 and 2TS22C ATAC-seq experiments were merged with BEDTools (Quinlan and Hall, 2010)
Replicate bam files were merged using SAMTools (Li et al., 2009) and converted to bigWig files using the deepTools 3.1.3 (Ramírez et al., 2016) function bamCoverage with settings ‘--normalizeUsingRPKM’
Genome_build: mm10
Supplementary_files_format_and_content: .bw, ZHBTc4_2TS22C_mergepeaks.bed, ZHBTc4_2TS22C_DE.xlsx contains DE values obtained from limma in accessible regions and features overlapping these regions

treatment_protocol: Cells were treated with 1 ug/ml doxycycline or left untreated for 26h/40h (2TS22C) or 24h (ZHBTc4)


title: ChIP_OCT4_SOX2ON_26h_2


title: ATAC_OCT4ON_S2iL_2


title: ATAC_OCT4OFF_S2iL_2


title: ChIP_BRG1_SOX2ON_26h_1


title: ChIP_OCT4_SOX2OFF_26h_2


title: ChIP_OCT4_SOX2ON_26h_1


title: ATAC_SOX2ON_26h_2


title: ATAC_OCT4ON_S2iL_1


title: ATAC_SOX2ON_40h_2

value: Untreated 40 hours


title: ChIP_H3K27ac_OCT4ON_S2iL_2


title: ATAC_SOX2OFF_40h_1


title: ATAC_SOX2OFF_26h_2


title: MeCP2_KO_60min_FP_PROseq_rep3

description:
Nascent RNA
FP_PROseq_WT_MeCP2_KO_0_20_40_60_min_mapped_to_all_genes_TSS.txt

data_processing:
Random hexanucleotide barcodes included in sequencing adaptors permitted the identification and removal of PCR duplicates using Clumpify (BBTools v37.90).
Reads were trimmed to 25 bp and mapped to the mm10 reference genome using Bowtie2 (v2.2.9).
Reads were converted to BED format using BEDTools (v2.26.0) and trimmed to the width of a single nucleotide at the second-to-3’ position, corresponding to the position of RNA Polymerase II before the incorporation of the terminal 11-biotin-NTP.
To quantify initiated Pol II signal, PRO-seq reads were counted in -500 to +500 bp of the TSS using bedtools map. Initiation rates were calculated as the linear fit of 0 minute, 20 minute, and 40 minute initiated Pol II PRO-seq signal over time using the lm function in R.
Genome_build: mm10
Supplementary_files_format_and_content: Table of raw PRO-seq read counts in TSS (-500bp to +500bp) for all genes.

extract_protocol:
One side of each forebrain was used for PRO-seq. Cells were permeabilized as described previously (Mahat et al., 2016), with minor modifications. Tissue was dounce homogenized in 5 mL cold PBS, then spun at 800g for 4 minutes at 4°C. The pellet was washed with 10 mL PBS, then spun at 800g for 4 minutes at 4°C. The pellet was resuspended in 1 mL Buffer W (10 mM Tris pH 8, 10 mM KCl, 250 mM sucrose, 5 mM MgCl2, 0.5 mM DTT, 10% glycerol) and then 9 mL Buffer P was added (Buffer W with 0.1% Igepal). Lysate was filtered through a 40μm cell strainer and spun at 800g for 4 minutes at 4°C. The pellet was resuspended in 1 mL Buffer W and then 9 mL Buffer P was added. Lysate was incubated on ice for 1 minute, then spun at 800g for 4 minutes at 4°C. The pellet was resuspended in 500 μL Buffer F (50 mM Tris pH 8, 40% glycerol, 5 mM MgCl2, 0.5 mM DTT) and spun at 1000g for 4 minutes at 4°C. The pellet was resuspended in 50 μL Buffer F with 0.5 μL RNase inhibitor (SUPERase In, Ambion), flash frozen, and stored at -80°C. PRO-seq RNA purification was performed as previously described (Kwak et al., 2013; Mahat et al., 2016). Frozen chromatin was thawed on ice and combined with 50 μL 2X Run-on Buffer (10 mM Tris-HCl pH 8.0, 5 mM MgCl2, 300 mM KCl, 40 μM Biotin-11-ATP, 40 μM Biotin-11-GTP, 40 μM Biotin-11-CTP, 40 μM Biotin-11-UTP, 1% Sarksosyl, 1 mM DTT, 0.8 units/μL SUPERase In RNase Inhibitor). The reaction was incubated at 37°C for 5 minutes and then quenched with 500 μL Trizol LS, combined with 130 μL chloroform, and centrifuged at 17,000g for 5 minutes at 4 °C. The aqueous layer containing RNA was combined with 1 mL ice-cold ethanol and 2.5 μL GlycoBlue (Invitrogen) and centrifuged at 17,000g for 15 minutes at 4 °C. The RNA pellet was washed in 75% ethanol, air-dried, and resuspended in 20 μL nuclease-free water. RNA was hydrolyzed by adding 5 μL 1 N NaOH and incubating for 4 minutes at 4°C, then neutralized with 30 μL 1 M Tris-HCl pH 7.0. Hydrolyzed RNA was run on a Micro Bio-Spin P-30 Column (Bio-Rad) to remove excess salts. Biotinylated RNA was purified with magnetic streptavidin beads (NEB) at room temperature for 20 minutes and washed 2 times each with 500 μL High-Salt (2 M NaCl, 50 mM Tris-HCl pH 7.4, 0.5% Triton X-100, 4 units/mL SUPERase In RNase Inhibitor), Binding (300 mM NaCl, 10 mM Tris-HCl pH 7.4, 0.1% Triton X-100, 4 units/mL SUPERase In RNase Inhibitor), and Low-Salt (5 mM Tris-HCl pH 7.4, 0.1% Triton X-100, 4 units/mL SUPERase In RNase Inhibitor) wash buffers. Beads were resuspended in 300 μL Trizol, and combined with 60 μL chloroform, and RNA was purified as above.
PRO-seq library preparation was performed as previously described (Kwak et al., 2013; Mahat et al., 2016). The dried RNA pellet was resuspended in 4 μL of 12.5 μM Reverse 3’ RNA adaptor and used to make a T4 RNA Ligase I reaction mix (5 μM Reverse 3’ RNA Adaptor, 1X T4 RNA Ligase I Buffer, 1 mM ATP, 10 units T4 RNA Ligase I, 10% PEG 8000, 2 units/μL SUPERase In RNase Inhibitor). The reaction was incubated overnight at 20°C. The ligated RNA was purified with magnetic streptavidin beads, washed, and extracted with Trizol as above. The RNA was treated with RNA 5' Pyrophosphohydrolase (RppH) to remove the 5’ cap (1X NEBuffer 2, 10 units RppH, 0.2 units/μL SUPERase In RNase Inhibitor) and incubated for 1 hour at 37°C. A hydroxyl repair reaction mix (1X PNK Buffer, 1 mM ATP, 25 units PNK, 0.2 units/μL SUPERase In RNase Inhibitor) was added directly to the Rpph reaction and incubated for an additional hour at 37°C. RNA was extracted with Trizol as above. The dried RNA pellet was resuspended in 4 μL of 12.5 μM Reverse 5’ RNA adaptor and used to make a T4 RNA Ligase I reaction mix (5 μM Reverse 5’ RNA Adaptor, 1X T4 RNA Ligase I Buffer, 1 mM ATP, 10 units T4 RNA Ligase I, 10% PEG 8000, 2 units/μL SUPERase In RNase Inhibitor). The reaction was incubated overnight at 20°C. The ligated RNA was purified with magnetic streptavidin beads, washed, and extracted with Trizol as above. The resulting RNA library was reverse transcribed using SuperScript III Reverse Transcriptase (Invitrogen). The cDNA libraries were amplified using Q5 DNA Polymerase (NEB) for 14 cycles or more, as determined by a test amplification with diluted cDNA. Amplified libraries were purified on Agencourt RNAClean XP beads.
PRO-seq

treatment_protocol: Flavopiridol hydrochloride (Tocris Bioscience) was prepared at 4 mg/mL in a 10% DMSO solution in PBS and injected intraperitoneally at a dose of 50 mg/kg into 8-week-old male WT or MeCP2 KO mice. 20, 40, or 60 minutes after flavopiridol injection, forebrain tissue was dissected and flash frozen. For the “0 minute” timepoint, mice were injected with a control solution of 10% DMSO in PBS and dissected after 40 minutes.

value: 8 weeks

value: Male

value: MeCP2 KO

tag: fp treatment

value: 60 minutes


title: ATAC_SOX2ON_40h_1


title: MeCP2_KO_60min_FP_PROseq_rep2


title: ATAC_SOX2OFF_26h_1


title: MeCP2_KO_60min_FP_PROseq_rep1


title: MeCP2_KO_40min_FP_PROseq_rep3

value: 40 minutes


title: MeCP2_KO_40min_FP_PROseq_rep1


title: MeCP2_KO_40min_FP_PROseq_rep2


title: ATAC_OCT4OFF_S2iL_1


title: MeCP2_KO_20min_FP_PROseq_rep1

value: 20 minutes


title: MeCP2_KO_0min_FP_PROseq_rep3

value: 0 minutes


title: MeCP2_KO_0min_FP_PROseq_rep1


title: MeCP2_WT_60min_FP_PROseq_rep3

value: WT


title: ATAC_SOX2ON_26h_1


title: MeCP2_WT_20min_FP_PROseq_rep2


title: MeCP2_WT_20min_FP_PROseq_rep3


title: MeCP2_WT_40min_FP_PROseq_rep2


title: MeCP2_WT_0min_FP_PROseq_rep2


title: MeCP2_WT_40min_FP_PROseq_rep1


title: MeCP2_WT_0min_FP_PROseq_rep3


title: MeCP2_KO_20min_FP_PROseq_rep2